From ksupreet6 at gmail.com  Thu Jan 19 09:43:47 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Thu, 19 Jan 2012 09:43:47 -0500
Subject: [Mristudio-users] need help!!!
Message-ID: <CAMUw5-vFsmaCP6pChWwNNnnztMDiss3d4g-HYOYh-kwij7=TrQ@mail.gmail.com>

Hi DTI experts
                           I just ran into a problem for DTI image viewing
in DTI studio. I go a data on a CD which has the following parameters:
256 x 256 x21 and 26 image blocks. I ran the AIR function and saved the
images as .rec format. But I am not able to procecced further to fiber
tracking
as i am not able to view the DTI  images.
please help me with this.

I'll appreciate your help.

Thanks

Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From sodhiks at gmail.com  Thu Jan 19 10:16:33 2012
From: sodhiks at gmail.com (kushaljit sodhi)
Date: Thu, 19 Jan 2012 20:46:33 +0530
Subject: [Mristudio-users] need help!!!
In-Reply-To: <CAMUw5-vFsmaCP6pChWwNNnnztMDiss3d4g-HYOYh-kwij7=TrQ@mail.gmail.com>
References: <CAMUw5-vFsmaCP6pChWwNNnnztMDiss3d4g-HYOYh-kwij7=TrQ@mail.gmail.com>
Message-ID: <CA+sTpfF_4TFoJdPvsqa7d=A3_r4=FD-7ySXRn4-JBMUukg5ahw@mail.gmail.com>

We have 3.0 T MRI siemens unit.
We have a loaded EPI sequence for DTI.
HOwever, it does not have software for quantitative DTI.

How do I calculate Quantitative DTI ? Is a software for
these calculations available online?

Thanks
Kushaljit

On Thu, Jan 19, 2012 at 8:13 PM, Supreet kaur <ksupreet6 at gmail.com> wrote:

> Hi DTI experts
>                            I just ran into a problem for DTI image viewing
> in DTI studio. I go a data on a CD which has the following parameters:
> 256 x 256 x21 and 26 image blocks. I ran the AIR function and saved the
> images as .rec format. But I am not able to procecced further to fiber
> tracking
> as i am not able to view the DTI  images.
> please help me with this.
>
> I'll appreciate your help.
>
> Thanks
>
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>


-- 
Kushaljit Singh  Sodhi
MD,FICR
Associate Professor,
Deptt of Radiodiagnosis,
PGIMER,Chandigarh,160012
INDIA.
Ph-0091-9914208634
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From ksupreet6 at gmail.com  Fri Jan 27 12:15:32 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Fri, 27 Jan 2012 12:15:32 -0500
Subject: [Mristudio-users] DTI gradient table
Message-ID: <CAMUw5-vJOTCOH3fpB+uvR8ns5MjtCP-BNVy=Pv91qjN3G2LPAw@mail.gmail.com>

Dear DTI experts,
                             I have a DTI data with 25 gradient directions,
what gradient table should we use for that?
Its a Siemens 3T scanner...
I'll appreciate your help.

Thanks

Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From swrhxy at 126.com  Fri Jan 27 13:18:45 2012
From: swrhxy at 126.com (=?GBK?B?u6rQ+NpT?=)
Date: Sat, 28 Jan 2012 02:18:45 +0800 (CST)
Subject: [Mristudio-users] DTI gradient table
In-Reply-To: <CAMUw5-vJOTCOH3fpB+uvR8ns5MjtCP-BNVy=Pv91qjN3G2LPAw@mail.gmail.com>
References: <CAMUw5-vJOTCOH3fpB+uvR8ns5MjtCP-BNVy=Pv91qjN3G2LPAw@mail.gmail.com>
Message-ID: <52ab9e03.9217.135206417ec.Coremail.swrhxy@126.com>

Dear Supreet kaur:
         Use  dcm2niigui.exe ( you could found it in MRICrond) to convert your DTI data and you would found the gradient table. Open it as a *.txt file. ~
--


Xu-Yun Hua, M.D.

Hand Surgery Department

Huashan Hospital

12 Middle Wulumuqi Road, 200040,Shanghai

China

E-mail: swrhxy at 126.com

At 2012-01-28 01:15:52,"Supreet kaur" <ksupreet6 at gmail.com> wrote:

Dear DTI experts,
                             I have a DTI data with 25 gradient directions, what gradient table should we use for that?
Its a Siemens 3T scanner...
I'll appreciate your help.
 
Thanks


Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509

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From ksupreet6 at gmail.com  Fri Jan 27 16:27:04 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Fri, 27 Jan 2012 16:27:04 -0500
Subject: [Mristudio-users] DTI gradient table
In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F2D655C7B07@RAD-EXCH1.win.ad.jhu.edu>
References: <CAMUw5-vJOTCOH3fpB+uvR8ns5MjtCP-BNVy=Pv91qjN3G2LPAw@mail.gmail.com>
	<145933A2BE9E4F48AE079A201379BF2F2D655C7B06@RAD-EXCH1.win.ad.jhu.edu>
	<CAMUw5-vYHLVV6SqkvM_p2QEV14kF7deNGJhGKW+6bvSN73KwzA@mail.gmail.com>
	<145933A2BE9E4F48AE079A201379BF2F2D655C7B07@RAD-EXCH1.win.ad.jhu.edu>
Message-ID: <CAMUw5-s=RGMz8SifbHy9dpj3eNRKNreDOm=cRTEm_87jQP+TxQ@mail.gmail.com>

Hi Hangji,
               I figured out that it was Philips 3T scanner (but we still
don't know what kind, though it is out of state scanner images we got), and
it has 25 gradient directions (including the bo image). I used the
following gradient table:

0: 0, 0, 0

1: 0.532212965784, 0.104012540712, -0.840196852187

2: 0.250139840140, -0.721834058886, 0.645279514479

3: -0.633506688611, -0.753135632571, -0.177358378534

4: -0.218922463231, 0.850392517067, 0.478440719431

5: -0.413149806364, -0.780294228218, 0.469519067675

6: 0.734236034340, -0.661803691272, 0.151371463942

7: 0.936469940841, 0.054189066241, 0.346536570943

8: -0.333112408327, -0.242859001882, 0.911073887576

9: 0.103315488089, -0.991677012629, -0.076828461807

10: -0.926539655526, 0.372983070696, -0.049070313963

11: 0.801488967040, 0.543143312217, -0.250221458126

12: -0.916836769339, -0.261947685782, 0.301320009791

13: -0.537755795155, 0.438027927278, -0.720382009562

14: -0.213559057919, -0.664684481487, -0.715951862105

15: -0.124138610474, -0.051815651202, -0.990911067493

16: 0.273979937314, 0.960273112918, -0.053014550417

17: -0.443315490443, 0.878048334487, -0.180284492503

18: 0.024170841904, 0.368771526312, 0.929205753202

19: 0.568365159741, 0.637098308775, 0.520640749604

20: 0.930930389545, -0.168157726945, -0.324178328533

21: -0.825458835938, -0.182178469442, -0.534255290516

22: 0.472597880311, -0.629557481175, -0.616691674520

23: 0.504263360030, -0.129264527496, 0.853820323992

24: 0.149335563174, 0.688742589708, -0.709459325610

25: -0.694717409994, 0.344411933027, 0.631465074759
 But unfortunately, the image quality looks very bad for the color map
images...
I'll appreciate your reply.

Thanks
Supreet.

On Fri, Jan 27, 2012 at 2:22 PM, Hangyi Jiang <hjiang at jhmi.edu> wrote:

> hi,Supreet
>
>  seems that your dataset has not being loaded in correctly,  or they are
> not in Siemens Mosaic format.
>
> you said that the dataset has " 25 gradient directions", right?  if so,
> you will get 25 image volumes (and maybe more,  since B0 images) after
> "File->Dti Mapping -> Siemens Mosaic...".  please double check if the
> images are loaded in correctly before you figure out the gradient table.
>
> regards,
>
> hangyi
>
>
>
>
>
> ________________________________________
> From: Supreet kaur [ksupreet6 at gmail.com]
> Sent: Friday, January 27, 2012 1:31 PM
> To: Hangyi Jiang
> Subject: Re: DTI gradient table
>
> Hi Hangyi,
>                        When I do the steps as you suggested , it gives a
> the following: I don't know what to do at this point, Please help
>
> 0: 0.000000, 0.000000, 0.000000, 1703965
> 1: 0.000000, 0.000000, 0.000000, 524297
> 2: 0.000000, 0.000000, 0.000000, 1507345
> 3: 0.000000, 0.000000, 0.000000, 851980
> 4: 0, 0, 0, 0
> 5: 0, 0, 0, 0
> 6: 0, 0, 0, 0
> 7: 0, 0, 0, 0
> 8: 0, 0, 0, 0
> 9: 0, 0, 0, 0
> 10: 0, 0, 0, 0
> 11: 0, 0, 0, 0
> 12: 0, 0, 0, 0
> 13: 0, 0, 0, 0
> 14: 0, 0, 0, 0
> 15: 0, 0, 0, 0
> 16: 0, 0, 0, 0
> 17: 0, 0, 0, 0
> 18: 0, 0, 0, 0
> 19: 0, 0, 0, 0
> 20: 0, 0, 0, 0
> 21: 0, 0, 0, 0
> 22: 0, 0, 0, 0
> 23: 0, 0, 0, 0
> 24: 0, 0, 0, 0
> 25: 0, 0, 0, 0
> 26: 0, 0, 0, 0
> 27: 0, 0, 0, 0
> 28: 0, 0, 0, 0
> 29: 0, 0, 0, 0
> 30: 0, 0, 0, 0
> 31: 0, 0, 0, 0
> 32: 0, 0, 0, 0
> 33: 0, 0, 0, 0
> 34: 0, 0, 0, 0
> 35: 0, 0, 0, 0
> 36: 0, 0, 0, 0
> 37: 0, 0, 0, 0
> 38: 0, 0, 0, 0
> 39: 0, 0, 0, 0
> 40: 0, 0, 0, 0
> 41: 0, 0, 0, 0
> 42: 0, 0, 0, 0
> 43: 0, 0, 0, 0
> 44: 0, 0, 0, 0
> 45: 0, 0, 0, 0
> 46: 0, 0, 0, 0
> 47: 0, 0, 0, 0
> 48: 0, 0, 0, 0
> 49: 0, 0, 0, 0
> 50: 0, 0, 0, 0
> 51: 0, 0, 0, 0
> 52: 0, 0, 0, 0
> 53: 0, 0, 0, 0
> 54: 0, 0, 0, 0
> 55: 0, 0, 0, 0
> 56: 0, 0, 0, 0
> 57: 0, 0, 0, 0
> 58: 0, 0, 0, 0
> 59: 0, 0, 0, 0
> 60: 0, 0, 0, 0
> 61: 0, 0, 0, 0
> 62: 0, 0, 0, 0
> 63: 0, 0, 0, 0
>
> On Fri, Jan 27, 2012 at 1:11 PM, Hangyi Jiang <hjiang at jhmi.edu<mailto:
> hjiang at jhmi.edu>> wrote:
>
> if the dataset is saved as Siemens Mosaic format, you can try to get the
> gradients from file header.
> try this:  File->DtiMapping -> Siemens Mosaic ->.. specify the file name
> (actually folder name).. clicking "get gradients from file header"
> button....;
>
> let me know if you have any problems..
>
> hangyi
>
> hangyi
>
>
>
>
>
>
> ________________________________________
> From: Supreet kaur [ksupreet6 at gmail.com<mailto:ksupreet6 at gmail.com>]
> Sent: Friday, January 27, 2012 12:15 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Cc: Hangyi Jiang; Susumu Mori
> Subject: DTI gradient table
>
> Dear DTI experts,
>                            I have a DTI data with 25 gradient directions,
> what gradient table should we use for that?
> Its a Siemens 3T scanner...
> I'll appreciate your help.
>
> Thanks
>
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509<tel:%28614%29355-3509>
>
>
>
>
> --
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>


-- 
Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From ksupreet6 at gmail.com  Mon Jan 30 12:19:04 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Mon, 30 Jan 2012 12:19:04 -0500
Subject: [Mristudio-users] GE gradient table
Message-ID: <CAMUw5-v9FVnsK2dNfBJYp5F=g97=Y2K34aYa3WztbE8FoJ0wzw@mail.gmail.com>

Hi DTI experts,
                           Our hospital is using GE 3T (HDXT) at 16.0
platform with 25 directions . But unfortunatley they don't have a right
gradient table for it.
Could you please suggest to provide the right gradient table.

I'll appreciate your help.

Thanks

Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From joeh at cis.jhu.edu  Thu Feb  2 19:18:03 2012
From: joeh at cis.jhu.edu (joeh at cis.jhu.edu)
Date: Thu, 02 Feb 2012 19:18:03 -0500 (EST)
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) Software
	Beta 48 Announcement
Message-ID: <35562.173.69.187.127.1328228283.squirrel@webmail.cis.jhu.edu>

Computational Anatomy Works (CAWorks) Software Beta 48 Announcement

CAWorks beta 48 is now available for windows 32 and 64 bit, mac osx, and
linux 32 and 64 bit

The new version includes


Addition of multiple contour display on data slices for volume and surfaces

Improvements to contour slices display to optimize colors as well as

further optimization of color space seperation for multiple surface display

Addition of heart landmark type

Improvements to anaylze and nifti reader and writers

Bug fixes and improvements for freesurfer file readers and writers and itk
filters

CAWorks is available through mristudio.org under:

   https://www.mristudio.org/download/binaries/caworks/

The software application Computational Anatomy Works (CAWorks) was
developed to support Computational Anatomy and shape analysis. The
capabilities of CAWorks include:

   1. Interactive landmark placement to create segmentation (mask) of
desired region of interest

   2. Specialized landmark placement plugins for subcortical structures
such as hippocampus and amygdala

   3. Support for multiple Medical Imaging data formats, such as Nifti,
Analyze, Freesurfer, DICOM and landmark data

   4. Quadra Planar view visualization

   5. Shape Analysis plugin modules, such as Large Deformation
Diffeomorphic Metric Mapping (LDDMM)

Current enhancements to CAWorks have focused on interactive support for
landmarking of subcortical structures. Specific plugins are available for
landmark placement of the hippocampus, amygdala and entorhinal cortex
regions. After landmarking is completed, CAWorks facilitates submission
for automated segmentation processing. CAWorks is being used by the
Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
Localization and Biomedical Informatics Research Network (BIRN) projects.

CAWorks extends ParaView, an open source, multi-platform, freely available
program for parallel, interactive, scientific visualization. An important
visualization tool for TeraGrid researchers, its client-server
architecture facilitates remote visualization of datasets and the
generation of level of detail (LOD) models that maintain interactive frame
rates for large datasets.

Tutorials describing CAWorks for the ROI feature are located at:

    http://caportal.cis.jhu.edu/tutorials


If you have questions regarding this software, please put CAWorks in your
subject line for the mristudio-users mailing list.

Thanks!
CAWorks Development Team


From lucas_lessa at yahoo.com.br  Fri Feb  3 08:00:24 2012
From: lucas_lessa at yahoo.com.br (Lucas Lessa)
Date: Fri, 03 Feb 2012 11:00:24 -0200
Subject: [Mristudio-users] Normalize DTI studies from different scanners
Message-ID: <C6358A10-6208-42D9-8122-3250D965462C@yahoo.com.br>

Dear friends,

I'm trying to compare the changes in DTI in a case.
I have several studies from one subject, all of them have DTI, but I can't observe changes, probably because of the differences in the studies.
Some studies were made in Philips Achieva 1,5T and other in a GE HD 1,5T.
The good thing is that all studies have 33 directions.
But it's the only similarity.
Can I normalize these studies?
Thank you.

Lucas Lessa.

From jcoughl2 at jhmi.edu  Fri Feb  3 19:56:46 2012
From: jcoughl2 at jhmi.edu (Jennifer Coughlin)
Date: Fri, 03 Feb 2012 19:56:46 -0500
Subject: [Mristudio-users] question please
In-Reply-To: <7250d5b15430.4cbd95a4@johnshopkins.edu>
References: <927603.69159.qm@web113319.mail.gq1.yahoo.com>
	<7250d5b15430.4cbd95a4@johnshopkins.edu>
Message-ID: <C8E1198ED9D83740B06F78247E7B46840ADCE6FA57@BAYEXCH-VS1.win.ad.jhu.edu>

Xin,
I do not know how to register for a login/password so that I may download ROI Editor.  I have tried before, but want it on a new computer.  Please direct me to the correct page so that I can register and download this sofware.

Many thanks, 
Jenn Coughlin

________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li [xli16 at jhmi.edu]
Sent: Tuesday, October 19, 2010 12:57 PM
To: DTI Studio, ROI Editor,     DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] question please

Hello,

The Microsoft Visual Studio Redistribution package needs to be installed on your machine before you run DtiStudio.

You can download the redistribution package at https://www.mristudio.org/wiki/installation. If you want to run DtiStudio_latest_x86.exe, please download vcredist_x86.exe. If you want to run DtiStudio_latest_x64.exe, please download vcredist_x64.exe.


Xin


----- Original Message -----
From: hadi sabahi <sabahihadi at yahoo.com>
Date: Tuesday, October 19, 2010 10:33 am
Subject: [Mristudio-users] question please
To: mristudio-users at mristudio.org


> Hello, I have problem in launch the dtisudio, when I click the program
> for running , I get this error : "the application has failed to start
> beacase its side-by-side configuration is incorrect, please see the
> application event log for more detail".
>
>  How can I solve this problem ? please.
>
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

From jcoughl2 at jhmi.edu  Fri Feb  3 20:00:02 2012
From: jcoughl2 at jhmi.edu (Jennifer Coughlin)
Date: Fri, 03 Feb 2012 20:00:02 -0500
Subject: [Mristudio-users] basic login/registration request
Message-ID: <C8E1198ED9D83740B06F78247E7B46840ADCE6FA58@BAYEXCH-VS1.win.ad.jhu.edu>


Xin,
I do not know how to register for a login/password so that I may download ROI Editor.  I have tried before, but want it on a new computer.  Please direct me to the correct page so that I can register and ultimately download this sofware.

Many thanks,
Jenn Coughlin

From xli16 at jhmi.edu  Sat Feb  4 16:20:29 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Sat, 04 Feb 2012 16:20:29 -0500
Subject: [Mristudio-users] basic login/registration request
In-Reply-To: <C8E1198ED9D83740B06F78247E7B46840ADCE6FA58@BAYEXCH-VS1.win.ad.jhu.edu>
References: <C8E1198ED9D83740B06F78247E7B46840ADCE6FA58@BAYEXCH-VS1.win.ad.jhu.edu>
Message-ID: <7190f14c6983.4f2d5acd@johnshopkins.edu>

Hello Jennifer,

Please register at https://www.mristudio.org/register/user_register.php . If you have already registered before, please go to https://www.mristudio.org/register/forgetpassword.php and https://www.mristudio.org/register/forgetusername.php to get your username and password back. Then you can use your username and password to download the software.


Xin

----- Original Message -----
From: Jennifer Coughlin <jcoughl2 at jhmi.edu>
Date: Friday, February 3, 2012 8:01 pm
Subject: [Mristudio-users] basic login/registration request
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


>  Xin,
>  I do not know how to register for a login/password so that I may 
> download ROI Editor.  I have tried before, but want it on a new 
> computer.  Please direct me to the correct page so that I can register 
> and ultimately download this sofware.
>  
>  Many thanks,
>  Jenn Coughlin
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From susumu at mri.jhu.edu  Sat Feb  4 17:13:19 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 04 Feb 2012 17:13:19 -0500
Subject: [Mristudio-users] Normalize DTI studies from different scanners
In-Reply-To: <C6358A10-6208-42D9-8122-3250D965462C@yahoo.com.br>
References: <C6358A10-6208-42D9-8122-3250D965462C@yahoo.com.br>
Message-ID: <CAEq9apLb4G88x3FTVXC1X95n6QKcLBFwCZigvDW=QNETf3tcCw@mail.gmail.com>

I think cross-scanner normalization is a very tricky issue. It is always
related to your effect size. If you are following a stroke patients and
Warrarian degeneration causes 50% FA change, then you can just scan a
couple of subjects in both scanners and show the maximum difference could
be only within 10%. I think this is a valid logic. However, if you can't do
a comparison study like this (e.g. one of the scanners is out of
commission) and you are going after 5% effect size, then you have a very
tough case, especially for publication.

On Fri, Feb 3, 2012 at 8:00 AM, Lucas Lessa <lucas_lessa at yahoo.com.br>wrote:

> Dear friends,
>
> I'm trying to compare the changes in DTI in a case.
> I have several studies from one subject, all of them have DTI, but I can't
> observe changes, probably because of the differences in the studies.
> Some studies were made in Philips Achieva 1,5T and other in a GE HD 1,5T.
> The good thing is that all studies have 33 directions.
> But it's the only similarity.
> Can I normalize these studies?
> Thank you.
>
> Lucas Lessa.
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
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From ksupreet6 at gmail.com  Tue Feb 14 11:20:00 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Tue, 14 Feb 2012 11:20:00 -0500
Subject: [Mristudio-users] two-day session
Message-ID: <CAMUw5-tUwxZXviXzHhYQhjRqcD_rboaFh_OYpjTPHtSc=sgRZw@mail.gmail.com>

Hello DTI experts,
                                          I just need to know that when is
another two-day live session on DTI studio, Diffeomaps and ROI editor?
Could you please let me know so that I can attend it asap at John Hopkins.

Thanks
Supreet

Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From wangwtlong at gmail.com  Tue Feb 14 11:33:09 2012
From: wangwtlong at gmail.com (wt wang)
Date: Wed, 15 Feb 2012 00:33:09 +0800
Subject: [Mristudio-users] two-day session
In-Reply-To: <CAMUw5-tUwxZXviXzHhYQhjRqcD_rboaFh_OYpjTPHtSc=sgRZw@mail.gmail.com>
References: <CAMUw5-tUwxZXviXzHhYQhjRqcD_rboaFh_OYpjTPHtSc=sgRZw@mail.gmail.com>
Message-ID: <CAB+5SdL8bs8REc+sOsd8qwzPK4ixQ_9xN8Zrnq59rj2dQRxJKQ@mail.gmail.com>

Hi?friend?

I am not a DTI expert. I don't know anything about the session. So I can't
help you.

Sincerely,

Wentao Wang

2012/2/15 Supreet kaur <ksupreet6 at gmail.com>

> Hello DTI experts,
>                                           I just need to know that when is
> another two-day live session on DTI studio, Diffeomaps and ROI editor?
> Could you please let me know so that I can attend it asap at John Hopkins.
>
> Thanks
> Supreet
>
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Tue Feb 14 11:35:33 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 14 Feb 2012 11:35:33 -0500
Subject: [Mristudio-users] two-day session
In-Reply-To: <CAMUw5-tUwxZXviXzHhYQhjRqcD_rboaFh_OYpjTPHtSc=sgRZw@mail.gmail.com>
References: <CAMUw5-tUwxZXviXzHhYQhjRqcD_rboaFh_OYpjTPHtSc=sgRZw@mail.gmail.com>
Message-ID: <CAEq9apKdOU0EqiwDq6yqnS3gZ53RsC9LB8H8fK-CQMmmErkpTQ@mail.gmail.com>

https://www.mristudio.org/wiki/Tutorial

<https://www.mristudio.org/wiki/Tutorial>Please contact Xin Li if you are
interested in attending it and put your name in the waiting list.

On Tue, Feb 14, 2012 at 11:20 AM, Supreet kaur <ksupreet6 at gmail.com> wrote:

> Hello DTI experts,
>                                           I just need to know that when is
> another two-day live session on DTI studio, Diffeomaps and ROI editor?
> Could you please let me know so that I can attend it asap at John Hopkins.
>
> Thanks
> Supreet
>
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From ksupreet6 at gmail.com  Tue Feb 14 11:40:17 2012
From: ksupreet6 at gmail.com (Supreet kaur)
Date: Tue, 14 Feb 2012 11:40:17 -0500
Subject: [Mristudio-users] need help in retrieving my saved fibers!!!
Message-ID: <CAMUw5-sgKmJa1pOahmtYt7-dVYVgbhnWB2RZC3x1VbBVF5kP-A@mail.gmail.com>

Hello DTI experts,
                              I have a problem in retrieving my saved ROI
 fibers data in DTI studio. Here are the steps that I follow in saving my
Fibers after performing
the Fiber tracking:
(1) I saved my fibers in Analyze format (binary image).
(2) when I go back to load the fibers from the ROI operation tool menu, I
select the binary image from the menu box. Then the image parameter window
popps up, then I select the Raw data option (I make sure that all the image
parameters are the same as original).
(3) Then the message shows up saying "the image parameters in the file are
not consistent with the current ones"..and then i click yes to continue,
it shows me some odd fibers which weren't part of my oriniginal fiber track
trajectory (such as ILF, IFO, CC fibers which I saved originally).

I can save the fibers fine with save selected fibers options of the saving
the fiber track button, but I need to save the fibers in the analyze format
for our lab's
automation program that needs the analyze (binary image) format for the
images.

I'll truely appreciate your feedback and help on this matter.

Thanking you,
Sincerely,

Supreet kaur,
Biomedical research engineer,
Nationwide Childrens Hospital,
Columbus, OH
(614)355-3509
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From ziling653 at 126.com  Tue Feb 14 22:54:22 2012
From: ziling653 at 126.com (=?GBK?B?0OzTug==?=)
Date: Wed, 15 Feb 2012 11:54:22 +0800 (CST)
Subject: [Mristudio-users] about philips data processing
Message-ID: <62b1fef9.9f74.1357f259102.Coremail.ziling653@126.com>

Dear all,
  I have seen some papers doing correction for the head motion and eddy current of DTI data using FSL, then processing them with DTIstudio. It's ok to SIEMENS and GE. But when faced with PHILIPS data, I found that after eddy correction with FSL, the size of DTI images were doubled, so that I don't know how to import them into DTIstudio with original gradient table.
  Was there anything I might do wrong that could lead to this situation? Or are there any methods that can solve this problem except for using AIR in DTIstudio?



--

++++++++++++++++++++++++++++++
Yong Xu
major?developmental and educational psychology
Center for the Study of Applied Psychology, Key Laboratory of Mental Health and Cognitive Science of Guangdong Province, South China Normal University, Guangzhou 510631, P. R. China
Tel: +86 (0)15521159838
++++++++++++++++++++++++++++++
??
??????
?????????
???
??? ??? ??? ???? ?55?
???510631
???15521159838 (??, ??)
+++++++++++++++++++++++++
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From ziling653 at 126.com  Tue Feb 14 22:56:38 2012
From: ziling653 at 126.com (=?GBK?B?0OzTug==?=)
Date: Wed, 15 Feb 2012 11:56:38 +0800 (CST)
Subject: [Mristudio-users] about philips data processing
Message-ID: <2f0881a2.76c9.1357f27a24e.Coremail.ziling653@126.com>

Dear all,
  I have seen some papers doing correction for the head motion and eddy current of DTI data using FSL, then processing them with DTIstudio. It's ok to SIEMENS and GE. But when faced with PHILIPS data, I found that after eddy correction with FSL, the size of DTI images were doubled, so that I don't know how to import them into DTIstudio with original gradient table.
  Was there anything I might do wrong that could lead to this situation? Or are there any methods that can solve this problem except for using AIR in DTIstudio?
   Thank you  so much for any advices.


--

++++++++++++++++++++++++++++++
Yong Xu
major?developmental and educational psychology
Center for the Study of Applied Psychology, Key Laboratory of Mental Health and Cognitive Science of Guangdong Province, South China Normal University, Guangzhou 510631, P. R. China
Tel: +86 (0)15521159838
++++++++++++++++++++++++++++++
??
??????
?????????
???
??? ??? ??? ???? ?55?
???510631
???15521159838 (??, ??)
+++++++++++++++++++++++++

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From rajagov2 at ccf.org  Wed Mar 21 15:03:28 2012
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Wed, 21 Mar 2012 15:03:28 -0400
Subject: [Mristudio-users] Gray Matter DTI
Message-ID: <805446C63F89C84AB2C57FBAC64E430708D4E1@CCHSCLEXMB76.cc.ad.cchs.net>

Dear All,
 
I am interested in studying DTI changes (MD, I am wondering whether it will appropriate to study axial diffusivity also in the sense for instance  FA is more for WM than GM) in gray matter between control and our patient population. I am wondering what is way to segment white matter (WM) from gray matter (GM).
 
 I am also interested in extracting different lobes of the brain to study GM changes in each lobe. Basically based on our VBM results where I see GM volume changes I would like to study whether DTI measure MD changes in frontal, temporal, occipital and parietal lobes. If so, is there a way I can use the atlases to separate out different lobes of the brain.
 
Thanks
Venkat

 


===================================

 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2010).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
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From mimiz10 at hotmail.com  Wed Mar 21 15:45:31 2012
From: mimiz10 at hotmail.com (Christine Zakrzewski)
Date: Wed, 21 Mar 2012 19:45:31 +0000
Subject: [Mristudio-users] Gray Matter DTI
In-Reply-To: <805446C63F89C84AB2C57FBAC64E430708D4E1@CCHSCLEXMB76.cc.ad.cchs.net>
References: <805446C63F89C84AB2C57FBAC64E430708D4E1@CCHSCLEXMB76.cc.ad.cchs.net>
Message-ID: <BAY150-W34B4749C953DF1AB8CBF14B4400@phx.gbl>


You could use FSL to accomplish this. Use the TBSS scripts to calcuate FA and diffusivity.  I am also pretty sure once you have spatially normailzed the images, you can use Talairach Daemon to define your ROIs.  I am just assuming it has this functionality.  I have only ever done this with AFNI.  My next idea would be to use Freesurfer.  As for segmenting tissue types, I think FIRST is used for this.  Hope this helps.Chrissy
 Date: Wed, 21 Mar 2012 15:03:28 -0400
From: rajagov2 at ccf.org
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Gray Matter DTI







Dear All,
 
I am interested in studying DTI changes (MD, I am wondering whether it will appropriate to study axial diffusivity also in the sense for instance  FA is more for WM than GM) in gray matter between control and our patient population. I am wondering what is way to segment white matter (WM) from gray matter (GM).
 
 I am also interested in extracting different lobes of the brain to study GM changes in each lobe. Basically based on our VBM results where I see GM volume changes I would like to study whether DTI measure MD changes in frontal, temporal, occipital and parietal lobes. If so, is there a way I can use the atlases to separate out different lobes of the brain.
 
Thanks
Venkat
 
===================================
 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2010).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy.  Thank you.

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
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From Patrick.Sullivan4 at va.gov  Thu Mar 22 14:14:42 2012
From: Patrick.Sullivan4 at va.gov (Sullivan, Patrick M.)
Date: Thu, 22 Mar 2012 14:14:42 -0400
Subject: [Mristudio-users] Gradient Table From DICOM File Header
Message-ID: <C60D21E396966E479CA4219FD754A76AD4BD61FB9F@R04BYNMSGB1.r04.med.va.gov>

During the recent training it was mentioned that Philips DICOM Gradient Tables could be extracted directly from the file header, rather than input manually.  DTI Studio is clearly able to do this with our DICOM files because it does so automatically when using the "MRI View3D" option.  However, when I attempt to do the same in the "DTI Mapping" option (where one must manually enter or point to the gradient table) I find that the button is "greyed out" (i.e. cannot be clicked).  It would be very helpful if we could extract this information directly from our Philips DICOM files; does anyone know how to activate this option?  Thank you!

-Patrick
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From susumu at mri.jhu.edu  Thu Mar 22 18:48:57 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 22 Mar 2012 18:48:57 -0400
Subject: [Mristudio-users] Gradient Table From DICOM File Header
In-Reply-To: <C60D21E396966E479CA4219FD754A76AD4BD61FB9F@R04BYNMSGB1.r04.med.va.gov>
References: <C60D21E396966E479CA4219FD754A76AD4BD61FB9F@R04BYNMSGB1.r04.med.va.gov>
Message-ID: <CAEq9apLAwOHLH5t5xoqPFYahtFFJNmUY=9XkpWfHmCwozT2cuw@mail.gmail.com>

I think this function is activated only when you choose "Siemens DICOM" or
"Philips Extended DICOM" because generic DICOM files may not contain the
table information.

On Thu, Mar 22, 2012 at 2:14 PM, Sullivan, Patrick M. <
Patrick.Sullivan4 at va.gov> wrote:

> During the recent training it was mentioned that Philips DICOM Gradient
> Tables could be extracted directly from the file header, rather than input
> manually.  DTI Studio is clearly able to do this with our DICOM files
> because it does so automatically when using the ?MRI View3D? option.
> However, when I attempt to do the same in the ?DTI Mapping? option (where
> one must manually enter or point to the gradient table) I find that the
> button is ?greyed out? (i.e. cannot be clicked).  It would be very helpful
> if we could extract this information directly from our Philips DICOM files;
> does anyone know how to activate this option?  Thank you!
>
> -Patrick****
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From santoshyadav20076 at gmail.com  Thu Mar 22 19:00:20 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Thu, 22 Mar 2012 13:00:20 -1000
Subject: [Mristudio-users] eddy current correction and motion correction
	option
Message-ID: <CA+7fnM0Sacu0oMShv65XAPqUO7Q1HrJi6PEPs4ZFbEy7dZ3Myw@mail.gmail.com>

Hi DTI experts

Is DTI Studio, ROI Editor or DiffeoMap have eddy current correction, B0
correction and motion correction options? If they have then how much
effective?


With best regards

Santosh
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From susumu at mri.jhu.edu  Thu Mar 22 19:09:34 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 22 Mar 2012 19:09:34 -0400
Subject: [Mristudio-users] eddy current correction and motion correction
 option
In-Reply-To: <CA+7fnM0Sacu0oMShv65XAPqUO7Q1HrJi6PEPs4ZFbEy7dZ3Myw@mail.gmail.com>
References: <CA+7fnM0Sacu0oMShv65XAPqUO7Q1HrJi6PEPs4ZFbEy7dZ3Myw@mail.gmail.com>
Message-ID: <CAEq9apLQ=o1isaODN2No89LD5Ls5t+0hVYTzakcMhXOpiEo-1w@mail.gmail.com>

Please check this;

https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2

<https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2>The B0 correction
is possible if you have anatomical T2. Then you can do T2-b0 LDDMM. Please
check this paper;

Huang H, Ceritoglu C, Li X, Qiu A, Miller MI, van Zijl PC, Mori S.
Correction of B0 susceptibility induced distortion in diffusion-weighted
images using large-deformation diffeomorphic metric mapping. Magn Reson
Imaging 2008;26(9):1294-1302, PMC2612638

On Thu, Mar 22, 2012 at 7:00 PM, Santosh Yadav
<santoshyadav20076 at gmail.com>wrote:

> Hi DTI experts
>
> Is DTI Studio, ROI Editor or DiffeoMap have eddy current correction, B0
> correction and motion correction options? If they have then how much
> effective?
>
>
> With best regards
>
> Santosh
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Fri Mar 23 14:10:25 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 23 Mar 2012 14:10:25 -0400
Subject: [Mristudio-users] Gray Matter DTI
In-Reply-To: <805446C63F89C84AB2C57FBAC64E430708D4E1@CCHSCLEXMB76.cc.ad.cchs.net>
References: <805446C63F89C84AB2C57FBAC64E430708D4E1@CCHSCLEXMB76.cc.ad.cchs.net>
Message-ID: <CAEq9apJLD-VPpOo3tYzb+gd0WGSrBS8DK6+zZFd+6_j81Gprsw@mail.gmail.com>

Hi Venkat,

Please see "#3: Getting Started" and "#4" in
https://www.mristudio.org/wiki/user_manual/diffeomap.
This explains how you can parcellate brains into various structures and
also segment GM/WM.
Maybe you want to start from #4, explaining the entire pipeline.

I hope this is useful information for you.

Susumu

On Wed, Mar 21, 2012 at 3:03 PM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

>  Dear All,
>
> I am interested in studying DTI changes (MD, I am wondering whether it
> will appropriate to study axial diffusivity also in the sense for instance
>  FA is more for WM than GM) in gray matter between control and our patient
> population. I am wondering what is way to segment white matter (WM) from
> gray matter (GM).
>
>  I am also interested in extracting different lobes of the brain to study
> GM changes in each lobe. Basically based on our VBM results where I see GM
> volume changes I would like to study whether DTI measure MD changes in
> frontal, temporal, occipital and parietal lobes. If so, is there a way I
> can use the atlases to separate out different lobes of the brain.
>
> Thanks
> Venkat
>
>
>
> ===================================
>
>  Please consider the environment before printing this e-mail****
>
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2010).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From micdtiserver at gmail.com  Sun Mar 25 20:45:56 2012
From: micdtiserver at gmail.com (dti mic)
Date: Mon, 26 Mar 2012 10:45:56 +1000
Subject: [Mristudio-users] PhD position in brain development,
 Queensland Brain Institute, University of Queensland
Message-ID: <CAB97=HRes+G1hwuVjVTNygoQUZ8OKVRFfU1qKLTohkaTHn9wgA@mail.gmail.com>

 PhD position in brain development: Students with a background in
mathematics and computer science are especially encouraged to apply



*Queensland Brain Institute*

Researchers at the Queensland Brain Institute (QBI) work to discover the
cellular and molecular mechanisms that underlie the ability of the adult
brain to function.



Neuroscience is entering an era of accelerated discovery driven by the
application of new molecular, genetic and imaging technologies, which will
provide a deeper understanding of the regulation and function of the
nervous system. Significant advances in determining the molecular
regulation of nerve cell function and development will have a major impact
on our understanding of more complex areas such as behaviour, cognition,
ageing, neurological disease and mental illness.



Discoveries will also provide, for the first time, a real opportunity to
develop new therapeutics to treat mental and neurological diseases, which
account for a staggering 45 per cent of the disease burden in Australia. A
major goal for QBI researchers is to promote excellence in neuroscience by
fostering the exchange of ideas, establishing new collaborations and
augmenting partnerships that already exist within the wider UQ neuroscience
community.
The role

The development of the brain is characterised by the formation of
connections between neurons.  One of the largest fibre tracts in the brain
is the corpus callosum, which connects neurons in the left and right
cerebral hemispheres.  We are using molecular and genetic approaches as
well as state-of-the-art imaging technologies to discover how the brain is
wired up during development.  This work has direct implications for
understanding
how the brain functions and the pathophysiological mechanism of psychiatric
disorders, by integrating the multi-level network features obtained with
various functional and anatomical brain imaging technologies on different
scales.



A PhD project is available to utilise neuroimaging technologies to discover
mechanisms of brain wiring. The project involves developing neuroimage
analysis tools and software and applying them to biological problems.  In
this role the student will develop skills in developing computational
algorithms and computer programming in neuroimage analysis that could be
utilised in both basic research and clinical areas.


The person

Applicants should have an excellent GPA (>5.5 at UQ) and have a background
in mathematics and computer science, especially good knowledge on image
analysis. The student will be jointly supervised by Professor Linda
Richards (QBI) who is an expert in brain development and Professor Tianzi
Jiang (QBI, Centre for Advanced Imaging, UQ and Institute for Automation,
Chinese Academy of Sciences, Bejing) who is an expert in neuroimaging.



The ideal candidate will have primary experience in image analysis,
especially for diffusion MRI, but this is not essential. Outstanding C/C++
programming skills in Linux are highly desired. Secondary experience
with parallel
computing and in using a high performance cluster platform would be an
advantage.



Applicants should hold a First Class Honours degree or equivalent and be
eligible for an Australian Postgraduate Award (APA) or equivalent
international scholarship such as an International Postgraduate Research
(IPRS) award. The current scholarship rate for the Australian Postgraduate
Award is $23,728 per annum tax-free for three years. For further
information on scholarships please refer to
http://www.uq.edu.au/grad-school/scholarships-and-fees.
Enquiries

Please contact Professor Linda Richards on richards at uq.edu.au or the QBI
RHD student recruitment officer, Dr Blake Chapman, on qbistudents at uq.edu.au.




To submit an application for this role, use the *Apply* button below. All
applicants must supply the following documents: Cover letter, Academic
Results and Resume.



For information on completing the application process click
here<http://www.uq.edu.au/uqjobs/index.html?page=149386&pid=149313>
.



Applications close: April 15th, 2012
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From Patrick.Sullivan4 at va.gov  Tue Mar 27 11:46:25 2012
From: Patrick.Sullivan4 at va.gov (Sullivan, Patrick M.)
Date: Tue, 27 Mar 2012 11:46:25 -0400
Subject: [Mristudio-users] Multiple LDDMM Results
Message-ID: <C60D21E396966E479CA4219FD754A76AD4BE80DDB0@R04BYNMSGB1.r04.med.va.gov>

Hello,

When I enter multiple elasticity values, LDDMM returns one additional matrix.  (For instance if I enter all 3 possible values, I receive 4 maps, kimap, kimap001, kimap002, kimap003).  Visual examination of the results of these matrices makes me tentatively think that  kimap001-003 are for the three elasticity values I entered, while "kimap" is an average of these three.  Is this correct, or does the system work differently?  Thank you.

-Patrick
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From susumu at mri.jhu.edu  Wed Mar 28 07:42:46 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 28 Mar 2012 07:42:46 -0400
Subject: [Mristudio-users] Multiple LDDMM Results
In-Reply-To: <C60D21E396966E479CA4219FD754A76AD4BE80DDB0@R04BYNMSGB1.r04.med.va.gov>
References: <C60D21E396966E479CA4219FD754A76AD4BE80DDB0@R04BYNMSGB1.r04.med.va.gov>
Message-ID: <CAEq9apLNMU-3LNciTEDADww8ME1vAZWVDo2JtM4kvpiC7N7LSg@mail.gmail.com>

Hi Parick,

If you used cascading LDDMM with three alpha values, you gradually deform
the brain from the least elastic to the most elastic settings. The 001,
002, and 003 is the transformation at each step. If you use 001, 001+002,
and 001+002+003, you can see the transformation for gradual change.
001+002+003 = overall kimap.

Hope it helps.

susumu

On Tue, Mar 27, 2012 at 11:46 AM, Sullivan, Patrick M. <
Patrick.Sullivan4 at va.gov> wrote:

> Hello,****
>
> ** **
>
> When I enter multiple elasticity values, LDDMM returns one additional
> matrix.  (For instance if I enter all 3 possible values, I receive 4 maps,
> kimap, kimap001, kimap002, kimap003).  Visual examination of the results of
> these matrices makes me tentatively think that  kimap001-003 are for the
> three elasticity values I entered, while ?kimap? is an average of these
> three.  Is this correct, or does the system work differently?  Thank you.*
> ***
>
> ** **
>
> -Patrick****
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From liyiou at gmail.com  Mon Apr  2 17:27:09 2012
From: liyiou at gmail.com (Yiou Li)
Date: Mon, 02 Apr 2012 14:27:09 -0700
Subject: [Mristudio-users] Question about exporting the atlas in DiffeoMap
	to nifti/Analyze file
Message-ID: <CAPSKS5rtvqJdJJSXOBg87kCnouao4gt110E59Tj2_ZuAJ2OYqA@mail.gmail.com>

Dear MRIStudio experts,

I want to use the parcellation WM atlas (JHU-MNI-ss) as ROI for my own
analysis. However, I couldn't find a menu option in DiffeoMap to
export( or save as) the raw image to a standard imaging format
(nifti/Analyze)?

Could you please kinldy advise how can I do it if it's possible?

Best and thanks in advance!
Leo

From Katherine.Powers at va.gov  Fri Mar 30 14:25:59 2012
From: Katherine.Powers at va.gov (Powers, Katherine L. (Portland))
Date: Fri, 30 Mar 2012 11:25:59 -0700
Subject: [Mristudio-users] Too few slices being read- Philips
Message-ID: <6AA2909272E2104BABACDF236ABAECCD0D52E733@VHAV20MSGA1.v20.med.va.gov>

Hello DTI Studio users,

I was wondering if anyone else has had difficulties getting all slices
read into the DTI mapping. I'm attempting to analyze a Philips 32dir
overplus-Yes series with 64 slices from dicom files. I get a warning
pop-up that says:

 #_of_Images !=(#_of_gradients)x(#_of_repetitions)
 #_of_Images=204
 #_of_gradients=34
 #_of_repetitions=1 

Then the series appears oriented correctly with only 0-9 sag slices
rather than the full 0-63 slice sag acquisition. If I generate an FA
color map from these slices, it visually matches slices from the color
map generated on the Philips console so the following gradient table
appears to be working alright:

0: 0.000, 0.000, 0.000
 1: -0.465, 0.503, 0.728
 2: -0.527, 0.503, -0.685
 3: 0.711, 0.702, -0.031
 4: -0.620, 0.275, 0.735
 5: -0.173, 0.677, 0.715
 6: 0.055, 0.707, 0.705
 7: 0.455, 0.565, 0.688
 8: 0.721, 0.150, 0.677
 9: -0.620, 0.275, 0.734
 10: -0.260, 0.709, 0.655
 11: 0.327, 0.704, 0.630
 12: 0.548, 0.482, 0.683
 13: 0.736, 0.288, 0.612
 14: -0.680, 0.477, 0.556
 15: -0.444, 0.710, 0.546
 16: 0.582, 0.640, 0.501
 17: 0.732, 0.468, 0.495
 18: -0.702, 0.712, 0.031
 19: -0.726, 0.477, -0.495
 20: 0.687, 0.468, -0.556
 21: 0.454, 0.704, -0.546
 22: -0.702, 0.712, 0.023
 23: -0.661, 0.430, -0.616
 24: -0.703, 0.711, -0.024
 25: -0.316, 0.709, -0.631
 26: 0.270, 0.705, -0.656
 27: 0.711, 0.702, -0.039
 28: 0.681, 0.288, -0.674
 29: -0.703, 0.711, -0.019
 30: 0.009, 0.706, -0.708
 31: 0.711, 0.702, -0.042
 32: 0.676, -0.005, -0.737
 33: 100.000, 100.000, 100.000

Could it be that the calculated Philips volume is not being canceled
appropriately by the 33: 100,100,100 line? Are there set locations for
the dicom files for the calculated volume so I can simply excise them
manually if all else fails?

As an aside -the dicom file input also results in reduced # of slices
when using MRIview3D, but when I convert the dicom series into analyze
format I'm able to get volumes 0-33 with all slices showing. Since
Analyze format doesn't work with the DTImapping functionality, this is
informative but still a dead end for my tensor calculations.  

Any suggestions?

Thanks in advance for any assistance
-Katherine

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From xli16 at jhmi.edu  Mon Apr  2 17:47:49 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Mon, 02 Apr 2012 17:47:49 -0400
Subject: [Mristudio-users] Question about exporting the atlas in
	DiffeoMap	to nifti/Analyze file
In-Reply-To: <CAPSKS5rtvqJdJJSXOBg87kCnouao4gt110E59Tj2_ZuAJ2OYqA@mail.gmail.com>
References: <CAPSKS5rtvqJdJJSXOBg87kCnouao4gt110E59Tj2_ZuAJ2OYqA@mail.gmail.com>
Message-ID: <70f0e205189a2.4f79e645@johnshopkins.edu>

Please look at the attachment. The function you want is marked in red.


Xin

----- Original Message -----
From: Yiou Li <liyiou at gmail.com>
Date: Monday, April 2, 2012 5:27 pm
Subject: [Mristudio-users] Question about exporting the atlas in DiffeoMap	to nifti/Analyze file
To: mristudio-users at mristudio.org


> Dear MRIStudio experts,
>  
>  I want to use the parcellation WM atlas (JHU-MNI-ss) as ROI for my own
>  analysis. However, I couldn't find a menu option in DiffeoMap to
>  export( or save as) the raw image to a standard imaging format
>  (nifti/Analyze)?
>  
>  Could you please kinldy advise how can I do it if it's possible?
>  
>  Best and thanks in advance!
>  Leo
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 
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From bwahlt at gmail.com  Thu Apr  5 19:35:04 2012
From: bwahlt at gmail.com (Bernd Wahlt)
Date: Thu, 05 Apr 2012 19:35:04 -0400
Subject: [Mristudio-users] b0 files
Message-ID: <CABz-EnCWZ2TyCQiGYmAyS9O3yLaMWe_sXZWBScEkJjTQGug1cg@mail.gmail.com>

Dear DTI Experts,

I have two datasets, both 60 directions, in one dataset only 1 b0 was
collected and in the other i have 6 b0 images (same TE, TR etc.)
Could you comment on whether these two datasets can be combined? I am
worried about SNR issue but since both datasets have the
same number of directions I believe the SNR would be the same but not
sure about the effect of different number of b0 images
collected, especially on FA.

Thank you.

Bernd

From petersond at kennedykrieger.org  Thu Apr  5 14:55:55 2012
From: petersond at kennedykrieger.org (Peterson, Daniel)
Date: Thu, 05 Apr 2012 18:55:55 +0000
Subject: [Mristudio-users] A few questions about LDDMM transformations
Message-ID: <FC02439D1375C04F81C02894EAF99AC212D22691@kki-gsp-mail1.kki.org>

Hi All,

   I've got a couple of questions:

1) What kind of re-orientation strategy does DTI Studio use when reorienting tensors for an LDDMM transformation of tensor data. Is there a reference available somewhere? As I understand, this is a non-trivial problem.

2) What do the experts here feel about the feasibility of fiber-tracking in atlas-space? I know that this is traditionally considered undesireable, but do people think that perhaps with these more advanced methods, standard-space tractography could be feasable?

3) Are there any command-line tools available for working with LDDMM transformations in a scriptable, automated manner? It would help our productivity immensely if we could apply Hmaps and Kimaps from the command-line, without clicking on buttons. Being able to combine transformation matrices programmatically would be great as well.

Thanks so much,
-Dan



Disclaimer:
The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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From chasi at 163.com  Fri Apr  6 22:38:38 2012
From: chasi at 163.com (chasi)
Date: Sat, 07 Apr 2012 10:38:38 +0800 (CST)
Subject: [Mristudio-users]  Question about analyze FA value of fibers
Message-ID: <1f96d87a.4155.1368aaaea9f.Coremail.chasi@163.com>

Dear MRIStudio experts,

I want to use this software to obtain the mean FA value of my selected fiber. However, I couldn't find awayhow tosolve the above problem?

Could you please kinldy advise how can I do it if it's possible?

Best and thanks in advance

mandula
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From rachaelg.uh at gmail.com  Mon Apr  9 21:27:36 2012
From: rachaelg.uh at gmail.com (Rachael Gonzales)
Date: Mon, 09 Apr 2012 15:27:36 -1000
Subject: [Mristudio-users] DTI Studio Reference
Message-ID: <9C870D2E-EBB5-4B37-A573-5073FA50C10B@gmail.com>

Hello,

Could you please tell me the publication reference or author list that are preferred to be credited in publications for the following MRI Studio programs?

DTI Studio
DiffeoMap
ROIEditor

For example, for DTI Studio I was referring to the paper by Jiang and colleagues (2006), "DtiStudio: resource program for diffusion tensor computation and fiber bundle tracking" Comput Methods Programs Biomed 81:106-116.
 

Thanks!





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From susumu at mri.jhu.edu  Tue Apr 10 09:43:07 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 10 Apr 2012 09:43:07 -0400
Subject: [Mristudio-users] DTI Studio Reference
In-Reply-To: <9C870D2E-EBB5-4B37-A573-5073FA50C10B@gmail.com>
References: <9C870D2E-EBB5-4B37-A573-5073FA50C10B@gmail.com>
Message-ID: <CAEq9apLwH+CbwUmrhLMcEqm66ai6RULsVe85wk92S2egGDY3vg@mail.gmail.com>

Thank you for asking.

On Mon, Apr 9, 2012 at 9:27 PM, Rachael Gonzales <rachaelg.uh at gmail.com>wrote:

> Hello,
>
> Could you please tell me the *publication **reference* or *author list* that
> are *preferred* to be credited in publications for the following MRI
> Studio programs?
>
> *DTI Studio*
>

Jiang H, van Zijl PC, Kim J, Pearlson GD, Mori S. DtiStudio: resource
program for diffusion tensor computation and fiber bundle tracking. Comput
Methods Programs Biomed 2006;81(2):106-116, PMC


> *DiffeoMap*
> *ROIEditor*
>
> We don't have a publication specifically for these programs, but following
are the early papers that introduced many aspects of these programs.

Oishi K, Faria A, Jiang H, Li X, Akhter K, Zhang J, Hsu JT, Miller MI, van
Zijl PC, Albert M, Lyketsos CG, Woods R, Toga AW, Pike GB, Rosa-Neto P,
Evans A, Mazziotta J, Mori S. Atlas-based whole brain white matter analysis
using large deformation diffeomorphic metric mapping: application to normal
elderly and Alzheimer's disease participants. Neuroimage
2009;46(2):486-499, PMC2885858

Faria AV, Zhang J, Oishi K, Li X, Jiang H, Akhter K, Hermoye L, Lee SK,
Hoon A, Stashinko E, Miller MI, van Zijl PC, Mori S. Atlas-based analysis
of neurodevelopment from infancy to adulthood using diffusion tensor
imaging and applications for automated abnormality detection. Neuroimage
2010;52(2):415-428, PMC2886186

Faria AV, Hoon A, Stashinko E, Li X, Jiang H, Mashayekh A, Akhter K, Hsu J,
Oishi K, Zhang J, Miller MI, van Zijl PC, Mori S. Quantitative analysis of
brain pathology based on MRI and brain atlases--applications for cerebral
palsy. Neuroimage 2011;54(3):1854-1861, PMC3008311

>
>
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From susumu at mri.jhu.edu  Tue Apr 10 13:33:00 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 10 Apr 2012 13:33:00 -0400
Subject: [Mristudio-users] b0 files
In-Reply-To: <CABz-EnCWZ2TyCQiGYmAyS9O3yLaMWe_sXZWBScEkJjTQGug1cg@mail.gmail.com>
References: <CABz-EnCWZ2TyCQiGYmAyS9O3yLaMWe_sXZWBScEkJjTQGug1cg@mail.gmail.com>
Message-ID: <CAEq9apJbjKzNtCJnfLvo7URQvt2qAURv0tZXP3qfWA=md2h=-w@mail.gmail.com>

I can think of two ways.

1) you can average the 6b0s and create one b0. Then the file size of the
two datasets will be the same.
2) combine the two datasets into one file. You will get 6b0 + 60 direction
+ 1 b0 + 60 direction all in one file. Then your gradient table also needs
to follow this order. You can combine them by loading all data into one
DtiStudio window, select all 127 images for saving.

On Thu, Apr 5, 2012 at 7:35 PM, Bernd Wahlt <bwahlt at gmail.com> wrote:

> Dear DTI Experts,
>
> I have two datasets, both 60 directions, in one dataset only 1 b0 was
> collected and in the other i have 6 b0 images (same TE, TR etc.)
> Could you comment on whether these two datasets can be combined? I am
> worried about SNR issue but since both datasets have the
> same number of directions I believe the SNR would be the same but not
> sure about the effect of different number of b0 images
> collected, especially on FA.
>
> Thank you.
>
> Bernd
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From susumu at mri.jhu.edu  Thu Apr 12 20:05:21 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 12 Apr 2012 20:05:21 -0400
Subject: [Mristudio-users] A few questions about LDDMM transformations
In-Reply-To: <FC02439D1375C04F81C02894EAF99AC212D22691@kki-gsp-mail1.kki.org>
References: <FC02439D1375C04F81C02894EAF99AC212D22691@kki-gsp-mail1.kki.org>
Message-ID: <CAEq9apLz7bLtpueDRisyMA4S-i0gMjikpJ6JA8p2MypRVBWL_Q@mail.gmail.com>

I want to add some to Xin's reply.

On Thu, Apr 5, 2012 at 2:55 PM, Peterson, Daniel <
petersond at kennedykrieger.org> wrote:

>  Hi All,
>
>     I've got a couple of questions:
>
>  1) What kind of re-orientation strategy does DTI Studio use when
> reorienting tensors for an LDDMM transformation of tensor data. Is there a
> reference available somewhere? As I understand, this is a non-trivial
> problem.
>
>  2) What do the experts here feel about the feasibility of fiber-tracking
> in atlas-space? I know that this is traditionally considered undesireable,
> but do people think that perhaps with these more advanced methods,
> standard-space tractography could be feasable?
>
> If you want to transfer tractography results to an atlas space, you have
several options;
a) perform tractogrpahy in the native space, convert the trajectory
information into a binary masking information, and transform the binary
information into the atlas space. Repeat it for multiple subjects and
create population data.
b) Transform the image into the atlas space and perform tractography.
Repeat it for multiple subjects and create poulation data.
c) Transform the image in to the atlas space. Repeat it to for multiple
subjects and create population-averaged tensor map. Then perform
tractography.

#b and #c requires normalization of the tensor fields as described in your
question #1. I think all approaches are valid.



>  3) Are there any command-line tools available for working with LDDMM
> transformations in a scriptable, automated manner? It would help our
> productivity immensely if we could apply Hmaps and Kimaps from the
> command-line, without clicking on buttons. Being able to combine
> transformation matrices programmatically would be great as well.
>

We have not been very enthusiastic about automated pipelines both for
DtiStudio and MriStudio. This is because of quality control. We thought it
is very important to check each step of image processing and this is the
very reason we developed these programs, which are built for visual
inspection. The heart of the problem is, it is very difficult to come up
with quantitative QC report. We have been investing a lot of effort on the
automated pipeline with a good QC report. So far, it has been difficult to
get one which is as good as visual inspection. However, we are getting
there. I hope we can provide a good automated and quantitative QC for
DtiStudio this year and hopefully a first version for MriStudio. Then
automation itself would be an easy task for us.


>
>  Thanks so much,
> -Dan
>
>
> Disclaimer:
> The materials in this e-mail are private and may contain Protected Health
> Information. Please note that e-mail is not necessarily confidential or
> secure. Your use of e-mail constitutes your acknowledgment of these
> confidentiality and security limitations. If you are not the intended
> recipient, be advised that any unauthorized use, disclosure, copying,
> distribution, or the taking of any action in reliance on the contents of
> this information is strictly prohibited. If you have received this e-mail
> in error, please immediately notify the sender via telephone or return
> e-mail.
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From lwn_07 at yahoo.com.cn  Mon Apr 16 11:47:15 2012
From: lwn_07 at yahoo.com.cn (=?utf-8?B?5p2O5Y2r5aic?=)
Date: Mon, 16 Apr 2012 23:47:15 +0800 (CST)
Subject: [Mristudio-users] how to import the tracked fibers to matlab
	environment
Message-ID: <1334591235.17897.YahooMailClassic@web15601.mail.cnb.yahoo.com>

Dear all,
?
?Is there any we I can to import the tracked fiber imformation (all fibers, the result comes as *.dat)?to matlab? 
?
Best regards,
?
Weina
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From baiye at mail.ustc.edu.cn  Tue Apr 17 09:57:03 2012
From: baiye at mail.ustc.edu.cn (baiye at mail.ustc.edu.cn)
Date: Tue, 17 Apr 2012 21:57:03 +0800 (CST)
Subject: [Mristudio-users] Fiber-based transformation?
Message-ID: <13931739.916091334671023330.JavaMail.coremail@mailweb>

Hi!

Thank you for your time. I have some questions regarding DTI transformation.

Does DTI Studio or DiffeoMap provide a transformation option that is not voxel-based but fiber-based?

Or is there a human white matter fiber template that can be used to register with?

Thank you again! 

From zhaocailei197866 at 163.com  Tue Apr 10 11:12:03 2012
From: zhaocailei197866 at 163.com (zhaocailei197866)
Date: Tue, 10 Apr 2012 23:12:03 +0800 (CST)
Subject: [Mristudio-users] White Matter DTI
Message-ID: <4e2da4f3.30f68.1369ccfc27c.Coremail.zhaocailei197866@163.com>

I am interested in studying DTI changes with hydrocephalus in children. I am wondering which soft we should to use.
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From weinmaya at gmail.com  Wed Apr 18 03:11:09 2012
From: weinmaya at gmail.com (maya weinstein)
Date: Wed, 18 Apr 2012 09:11:09 +0200
Subject: [Mristudio-users] Question regarding b-value
Message-ID: <CACtX2Rtw0zVDbGpwH-Y9S-c_=x85UnJoRyO5znrrv18eu04W3Q@mail.gmail.com>

Hi MRI studio users,



In DTIStudio, in the "DTI Mapping" I noticed that the value I put in the
"b-value" affects the results I get in the statistics.

For example:

 b-val 700: Eig 0= 1.69E-03

b-val 70: Eig 0=0.0169

b-val 7: Eig 0= 0.1687



This seems to affect only the # of integers.



But- when I use *b-val -7* (minus seven), I get an entirely different
value:

*Eig0= 1.1812*

What does this mean? And is it a valid option?

I used this option (b val= -7) and I want to know if I need to re-calculate
the maps and reanalyze my data.



Thank you,

Maya


-- 
Maya Weinstein
Department of Psychology, Bar-Ilan University
Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
Tel-Aviv Sourasky Medical Center
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From weinmaya at gmail.com  Wed Apr 18 04:58:13 2012
From: weinmaya at gmail.com (maya weinstein)
Date: Wed, 18 Apr 2012 10:58:13 +0200
Subject: [Mristudio-users] Mean ADC map
Message-ID: <CACtX2RsA0GSL-HbLhQBRPNrbWXgWgZ=kJrWmgs7zfb6v2SABxQ@mail.gmail.com>

Hi MRIstudio users,

In the older versions when you calculated the ADC map there was a value for
a mean ADC map which is missing from the new version.
Is there an automatic way to calculate a mean ADC map?

Thanks,
Maya

-- 
Maya Weinstein
Department of Psychology, Bar-Ilan University
Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
Tel-Aviv Sourasky Medical Center
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From chris.s.mccarthy at gmail.com  Wed Apr 18 10:06:58 2012
From: chris.s.mccarthy at gmail.com (Christopher McCarthy)
Date: Wed, 18 Apr 2012 10:06:58 -0400
Subject: [Mristudio-users] CAWorks Amygdala Question
Message-ID: <CA+_rjOCqa9JH-SKaMzeEJHa7OEm1A8kRHXA3NoQCdEXRTB+hOw@mail.gmail.com>

Hello,

I am trying to get volumes for the Amygdala using the semi automated
landmarking process in CAworks.  I am having no trouble following the protocol
for landmarking<http://caportal.cis.jhu.edu/wiki/tutorials/amygdala/amygdala.html>
the
structure, however after I save the landmarks I am not sure what to do
next.  If anyone could point me towards the tutorial, or tell me the
procedure they follow I would be very appreciative!  Feel free to contact
me at the number listed below, or respond to the mailing list.

Thanks in advance!

Chris McCarthy
Center for Psychiatric Neuroimaging
SUNY Upstate Medical University
315-464-3269
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From susumu at mri.jhu.edu  Wed Apr 18 10:23:08 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 Apr 2012 10:23:08 -0400
Subject: [Mristudio-users] how to import the tracked fibers to matlab
 environment
In-Reply-To: <1334591235.17897.YahooMailClassic@web15601.mail.cnb.yahoo.com>
References: <1334591235.17897.YahooMailClassic@web15601.mail.cnb.yahoo.com>
Message-ID: <CAEq9apL_Wi2x-3aSQLBFuiYXTqWzHh+AZH4VmD8ZC3BTeZEORg@mail.gmail.com>

Hi Weina,

Please see FAQ#1 here (https://www.mristudio.org/wiki/faq).
I think you need to write a matlab code to read this format.

Susumu

On Mon, Apr 16, 2012 at 11:47 AM, ??? <lwn_07 at yahoo.com.cn> wrote:

> Dear all,
>
>  Is there any we I can to import the tracked fiber imformation (all
> fibers, the result comes as *.dat) to matlab?
>
> Best regards,
>
> Weina
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From tjab at jhu.edu  Wed Apr 18 10:56:02 2012
From: tjab at jhu.edu (Timothy Brown)
Date: Wed, 18 Apr 2012 10:56:02 -0400 (EDT)
Subject: [Mristudio-users] CAWorks Amygdala Question
In-Reply-To: <CA+_rjOCqa9JH-SKaMzeEJHa7OEm1A8kRHXA3NoQCdEXRTB+hOw@mail.gmail.com>
References: <CA+_rjOCqa9JH-SKaMzeEJHa7OEm1A8kRHXA3NoQCdEXRTB+hOw@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1204181053590.30981@io11.cis.jhu.edu>

Hello Chris,

Your next step would be to select a subject that you will use as a 
template for your study.  Then

1) Hand segment this subject (create binary mask of amygdala)
2) Create surface mesh from this binary mask
3) Create amygdala landmarks for this subject

Once you have performed the above steps you can use the remote processing 
feature of CAWorks to generate amygdala in your population.

http://caportal/wiki/tutorials/lddmm_remote_panel/tutorial.html

-Timothy

Timothy Brown                 email: timothy at cis.jhu.edu
Computational Anatomist       phone: 410.516.7551
Center for Imaging Science    fax:   410.516.4557
Johns Hopkins University
301 Clark Hall
3400 N. Charles Street
Baltimore, MD 21218


On Wed, 18 Apr 2012, Christopher McCarthy wrote:

> Hello,
>
> I am trying to get volumes for the Amygdala using the semi automated
> landmarking process in CAworks.  I am having no trouble following the protocol
> for landmarking<http://caportal.cis.jhu.edu/wiki/tutorials/amygdala/amygdala.html>
> the
> structure, however after I save the landmarks I am not sure what to do
> next.  If anyone could point me towards the tutorial, or tell me the
> procedure they follow I would be very appreciative!  Feel free to contact
> me at the number listed below, or respond to the mailing list.
>
> Thanks in advance!
>
> Chris McCarthy
> Center for Psychiatric Neuroimaging
> SUNY Upstate Medical University
> 315-464-3269
>

Timothy Brown                 email: timothy at cis.jhu.edu
Computational Anatomist       phone: 410.516.7551
Center for Imaging Science    fax:   410.516.4557
Johns Hopkins University
301 Clark Hall
3400 N. Charles Street
Baltimore, MD 21218

From susumu at mri.jhu.edu  Wed Apr 18 13:57:50 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 Apr 2012 13:57:50 -0400
Subject: [Mristudio-users] Question regarding b-value
In-Reply-To: <CACtX2Rtw0zVDbGpwH-Y9S-c_=x85UnJoRyO5znrrv18eu04W3Q@mail.gmail.com>
References: <CACtX2Rtw0zVDbGpwH-Y9S-c_=x85UnJoRyO5znrrv18eu04W3Q@mail.gmail.com>
Message-ID: <CAEq9apJDt2Dx7FrrVQxj3B=NQfsbzvEY4QX5XDkPz3Q=j5i3fg@mail.gmail.com>

Hi Maya,

It is expected that diffusion constant like Eig is inverse proportional to
the b-value such that b x diffusion constant is a constant.
If you type in non-physical number like negative b, I believe (Hangyi
please correct me if I'm wrong) DtiStudio use b=1.
In your case, b x D = 1.1812.

If you use b=1 for all the past data, you can simply divide the number with
b=700. This is the case of all the numbers with the diffusion constant unit
(mm^2/s) like Eigs, mean diffusivity, trace, etc. I believe the unit-less
numbers such as FA is not affected.

Susumu

On Wed, Apr 18, 2012 at 3:11 AM, maya weinstein <weinmaya at gmail.com> wrote:

> Hi MRI studio users,
>
>
>
> In DTIStudio, in the "DTI Mapping" I noticed that the value I put in the
> "b-value" affects the results I get in the statistics.
>
> For example:
>
>  b-val 700: Eig 0= 1.69E-03
>
> b-val 70: Eig 0=0.0169
>
> b-val 7: Eig 0= 0.1687
>
>
>
> This seems to affect only the # of integers.
>
>
>
> But- when I use *b-val -7* (minus seven), I get an entirely different
> value:
>
> *Eig0= 1.1812*
>
> What does this mean? And is it a valid option?
>
> I used this option (b val= -7) and I want to know if I need to
> re-calculate the maps and reanalyze my data.
>
>
>
> Thank you,
>
> Maya
>
>
> --
> Maya Weinstein
> Department of Psychology, Bar-Ilan University
> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
> Tel-Aviv Sourasky Medical Center
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Wed Apr 18 14:01:39 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 Apr 2012 14:01:39 -0400
Subject: [Mristudio-users] Mean ADC map
In-Reply-To: <CACtX2RsA0GSL-HbLhQBRPNrbWXgWgZ=kJrWmgs7zfb6v2SABxQ@mail.gmail.com>
References: <CACtX2RsA0GSL-HbLhQBRPNrbWXgWgZ=kJrWmgs7zfb6v2SABxQ@mail.gmail.com>
Message-ID: <CAEq9apKpDbuFTiEmNWy8yFPVpcHgTJp5XGWfW+5VEmtRxQVZxA@mail.gmail.com>

For ADC, please use "Trace". If you divide this by 3, it is what people
usually call "Mean Diffusivity", or "Average Diffusion Constant". Because
there are several nomenclature with inconsistent usage, we decided to use
"trace" which has no ambiguity. The mean ADC in the old version of
DtiStudio is "mean apparent diffusion constant" which is the mean of all
the "apparent (not average) diffusion constants" along various diffusion
encoding directions. I strongly recommend to use trace, not the "mean ADC"
in the older version.

On Wed, Apr 18, 2012 at 4:58 AM, maya weinstein <weinmaya at gmail.com> wrote:

> Hi MRIstudio users,
>
> In the older versions when you calculated the ADC map there was a value
> for a mean ADC map which is missing from the new version.
> Is there an automatic way to calculate a mean ADC map?
>
> Thanks,
> Maya
>
> --
> Maya Weinstein
> Department of Psychology, Bar-Ilan University
> Functional Brain Imaging Unit, Wohl Institute for Advanced Imaging,
> Tel-Aviv Sourasky Medical Center
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From drvikasdhiman.nimhans at gmail.com  Wed Apr 18 14:18:52 2012
From: drvikasdhiman.nimhans at gmail.com (Vikas Dhiman)
Date: Wed, 18 Apr 2012 11:18:52 -0700
Subject: [Mristudio-users] Vikas Dhiman wants to chat
Message-ID: <CA+bpy_ueD4Wz1ATsAryL5VXxrTVjxUV6a4Nb3Sm1F7wqLO+FSw@mail.gmail.com>

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From susumu at mri.jhu.edu  Wed Apr 18 14:23:16 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 Apr 2012 14:23:16 -0400
Subject: [Mristudio-users] Fiber-based transformation?
In-Reply-To: <13931739.916091334671023330.JavaMail.coremail@mailweb>
References: <13931739.916091334671023330.JavaMail.coremail@mailweb>
Message-ID: <CAEq9ap+Q-4KmHaT2j0U-=Qh6hrAVWmWOagTnuD4vJ7MhgEew3w@mail.gmail.com>

Do you mean, you want to align fiber-to-fiber between two brains?
If that is the question, no, we don't, but you can do the following.

For example, you can do tractography of the corticospinal tract (CST) in
two brains. Convert the tract information to a binary masking image, in
which pixels that contain the tract are "1" and the rests are "0".

>From the two brains, you can obtain two CST 1/0 binary images.

You can submit these two images by DiffeoMap for image matching. What will
happen then is, these two maps will be perfectly registered. Then you can
apply the transformation matrix to real images such as FA, b0, or
co-registered T1. However, I think this will register only the pixels that
belong to the CST and the rest of the brain is not well registered.

You can keep creating tracts like 10 more tracts. Then you will have 10 x 2
binary images from the two brains. You can submit 10-channel LDDMM throuth
DiffeoMap or you can combine the 10 binary images by assigning different
numbers; the CST is "1", SLF is "2", corpus callosum is "3", etc. Then you
can do 1-channel LDDMM. You can add FA map and do 2-channel LDDMM.

I thought of this kind of approach before but because the results of
tractography is quite noisy, I'm not sure if it improves the registration
accuracy....

On Tue, Apr 17, 2012 at 9:57 AM, <baiye at mail.ustc.edu.cn> wrote:

> Hi!
>
> Thank you for your time. I have some questions regarding DTI
> transformation.
>
> Does DTI Studio or DiffeoMap provide a transformation option that is not
> voxel-based but fiber-based?
>
> Or is there a human white matter fiber template that can be used to
> register with?
>
> Thank you again!
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From jonathan.park09 at gmail.com  Wed Apr 18 14:34:10 2012
From: jonathan.park09 at gmail.com (Jonathan Park)
Date: Wed, 18 Apr 2012 11:34:10 -0700
Subject: [Mristudio-users] Question from new user on finding transverse
	pontine fibers
Message-ID: <CAFE_30SuOoLaEVO0Nz0zJoR5sO8BmVQFLUHeDMHSoZTKuN+nFA@mail.gmail.com>

Hello Im a new user

I'm still figuring out how to use the program but will be using DTI
studio to measure the transverse pontine fibers. I was told these will
show up in red, is this always the case by default? Just trying to
figure out the best place to measure these fibers to get consistently
reproducible results. Thank you very much.

From susumu at mri.jhu.edu  Wed Apr 18 14:44:10 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 18 Apr 2012 14:44:10 -0400
Subject: [Mristudio-users] Question from new user on finding transverse
 pontine fibers
In-Reply-To: <CAFE_30SuOoLaEVO0Nz0zJoR5sO8BmVQFLUHeDMHSoZTKuN+nFA@mail.gmail.com>
References: <CAFE_30SuOoLaEVO0Nz0zJoR5sO8BmVQFLUHeDMHSoZTKuN+nFA@mail.gmail.com>
Message-ID: <CAEq9apLNjp2aX2SQ-m6MEzdTqiTeb_oAH9ceyhZ=FRLEM1t-sQ@mail.gmail.com>

Yes, if you did everything correct, the pontine fiber should appear red.

On Wed, Apr 18, 2012 at 2:34 PM, Jonathan Park <jonathan.park09 at gmail.com>wrote:

> Hello Im a new user
>
> I'm still figuring out how to use the program but will be using DTI
> studio to measure the transverse pontine fibers. I was told these will
> show up in red, is this always the case by default? Just trying to
> figure out the best place to measure these fibers to get consistently
> reproducible results. Thank you very much.
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From jonathan.park09 at gmail.com  Wed Apr 18 15:16:41 2012
From: jonathan.park09 at gmail.com (Jonathan Park)
Date: Wed, 18 Apr 2012 12:16:41 -0700
Subject: [Mristudio-users] Question from new user on finding transverse
 pontine fibers
In-Reply-To: <CAEq9apLNjp2aX2SQ-m6MEzdTqiTeb_oAH9ceyhZ=FRLEM1t-sQ@mail.gmail.com>
References: <CAFE_30SuOoLaEVO0Nz0zJoR5sO8BmVQFLUHeDMHSoZTKuN+nFA@mail.gmail.com>
	<CAEq9apLNjp2aX2SQ-m6MEzdTqiTeb_oAH9ceyhZ=FRLEM1t-sQ@mail.gmail.com>
Message-ID: <F5767C13-6E48-4874-AD9C-AC970CB88323@gmail.com>

Thank you very much. Sorry one more question I'm still new with this...should these fibers be in the pons belly? Sometimes my images weren't too clear. Thank you. 



On Apr 18, 2012, at 11:44, susumu mori <susumu at mri.jhu.edu> wrote:

> Yes, if you did everything correct, the pontine fiber should appear red.
> 
> On Wed, Apr 18, 2012 at 2:34 PM, Jonathan Park <jonathan.park09 at gmail.com> wrote:
> Hello Im a new user
> 
> I'm still figuring out how to use the program but will be using DTI
> studio to measure the transverse pontine fibers. I was told these will
> show up in red, is this always the case by default? Just trying to
> figure out the best place to measure these fibers to get consistently
> reproducible results. Thank you very much.
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
> 
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From mliu4 at ualberta.ca  Fri Apr 20 16:37:55 2012
From: mliu4 at ualberta.ca (Min Liu)
Date: Fri, 20 Apr 2012 14:37:55 -0600
Subject: [Mristudio-users] Does DTIstudio run on Mac?
Message-ID: <CAPje6jTB1xWNDcZQGkEuZ5fJPycBP1Eh+G-L3s_OY=aC3XA-PQ@mail.gmail.com>

Dear MRIStudio users,

Just a quick question to see if DTIstudio available for Mac. I didn't see
any downloadable version in the list. Thanks!

Min
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From susumu at mri.jhu.edu  Fri Apr 20 16:45:39 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 20 Apr 2012 16:45:39 -0400
Subject: [Mristudio-users] Does DTIstudio run on Mac?
In-Reply-To: <CAPje6jTB1xWNDcZQGkEuZ5fJPycBP1Eh+G-L3s_OY=aC3XA-PQ@mail.gmail.com>
References: <CAPje6jTB1xWNDcZQGkEuZ5fJPycBP1Eh+G-L3s_OY=aC3XA-PQ@mail.gmail.com>
Message-ID: <CAEq9apKeFQGo4ww5UK5CiF2O2PqeK_9opLyQBsXS5Q27uwnpyw@mail.gmail.com>

Sorry. No.

On Fri, Apr 20, 2012 at 4:37 PM, Min Liu <mliu4 at ualberta.ca> wrote:

> Dear MRIStudio users,
>
> Just a quick question to see if DTIstudio available for Mac. I didn't see
> any downloadable version in the list. Thanks!
>
> Min
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From yth0306 at yahoo.com.cn  Sat Apr 21 03:58:13 2012
From: yth0306 at yahoo.com.cn (Tianhua Yang)
Date: Sat, 21 Apr 2012 15:58:13 +0800 (CST)
Subject: [Mristudio-users] =?gb2312?b?ILvYuLSjuiAgRG9lcyBEVElzdHVkaW8gcnVu?=
 =?gb2312?b?IG9uIE1hYz8=?=
In-Reply-To: <CAEq9apKeFQGo4ww5UK5CiF2O2PqeK_9opLyQBsXS5Q27uwnpyw@mail.gmail.com>
References: <CAPje6jTB1xWNDcZQGkEuZ5fJPycBP1Eh+G-L3s_OY=aC3XA-PQ@mail.gmail.com>
	<CAEq9apKeFQGo4ww5UK5CiF2O2PqeK_9opLyQBsXS5Q27uwnpyw@mail.gmail.com>
Message-ID: <1334995093.22405.YahooMailNeo@web15003.mail.cnb.yahoo.com>




???? susumu mori <susumu at mri.jhu.edu>
???? "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org> 
????? 2012?4?21?, ???, ?? 4:45
??: Re: [Mristudio-users] Does DTIstudio run on Mac?


Sorry. No.


On Fri, Apr 20, 2012 at 4:37 PM, Min Liu <mliu4 at ualberta.ca> wrote:

Dear MRIStudio users, 
>
>
>Just a quick question to see if DTIstudio available for Mac. I didn't see any downloadable version in the list. Thanks!
>
>Min
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>
>

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From Jacquie.Hodge at albertahealthservices.ca  Fri Apr 20 16:19:09 2012
From: Jacquie.Hodge at albertahealthservices.ca (Jacquie Hodge)
Date: Fri, 20 Apr 2012 14:19:09 -0600
Subject: [Mristudio-users] tractography problems
Message-ID: <1DC4211314F7D9458B66A28F947F60B9D44C9C903D@EXMBX4C.crha.bewell.ca>

Hello,

I am having some difficulties and I'm not sure exactly what the problem is. I have attached a screen shot to show the ROI and the resulting fibers for CST that I get. The problem is I know there should be a full CST there. I have gone through the original images too see if there are any distorted ones to remove and they all look pretty clean. Do you have any suggestions as to what might be happening and how I can fix this?

Also, I have drawn another ROI further up the tract and there are fibers there (this is not shown on the picture I am sending you).

ANy help or suggestions is much appreciated as I do not want to lose this patient because of the scan!

Thank you so much!

Jacquie

Jacquie Hodge MSc candidate in Neuroscience, BSc
Neuroscience, University of Calgary
Research Assistant, Calgary Pediatric Stroke Program
Alberta Children's Hospital
2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
Phone: 403-955-7733 Fax: 403-955-2922
jacquie.hodge at albertahealthservices.ca
Program website: www.perinatalstroke.com
________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li [xli16 at jhmi.edu]
Sent: September 28, 2011 11:26 AM
To: DTI Studio, ROI Editor,     DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Issues with Running DTI studio x64

You are welcome.

The manuals and videos are at https://www.mristudio.org/wiki/user_manual


Xin

----- Original Message -----
From: uday bhaskar <udayanbhaskar at gmail.com>
Date: Wednesday, September 28, 2011 12:57 pm
Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Thank you.
>
>    Do you suggest some online tutorials for beginners.
>
>  --
>  Thanks,
>  Uday.
>
>  On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:
>
>  > Hello,
>  >
>  > It seems that you need to run vcredist_x64.exe on your computer
> first. The
>  > exe file is available at
>  >
>  > DtiStudio is a Microsoft Visual Studio applications. The Microsoft
> Visual
>  > Studio Redistribution package(vcredist_x64.exe) needs to be
> installed on
>  > your machine.
>  >
>  >
>  > Xin
>  >
>  >
>  > ----- Original Message -----
>  > From: uday bhaskar <udayanbhaskar at gmail.com>
>  > Date: Wednesday, September 28, 2011 12:45 pm
>  > Subject: [Mristudio-users] Issues with Running DTI studio x64
>  > To: mristudio-users at mristudio.org
>  >
>  >
>  > > Hi,
>  > >
>  > >      I am a beginner and a new user of DTI studio. I am having a
> problem
>  > >  running the DTIstudio-latest-x64. When I try to run it gives me
> an error
>  > >  saying "The application failed to start because its
>  > >  side-by-side configuration is incorrect".
>  > >
>  > >   Please let me know how to overcome this. Any help is appreciated.
>  > >
>  > >  --
>  > >  Thanks,
>  > >  Uday.
>  > > _______________________________________________
>  > >  mristudio-users mailing list
>  > >  mristudio-users at mristudio.org
>  > >
>  > >  Unsubscribe, send a blank email to:
>  > mristudio-users-unsubscribe at mristudio.org
>  > _______________________________________________
>  > mristudio-users mailing list
>  > mristudio-users at mristudio.org
>  >
>  > Unsubscribe, send a blank email to:
>  > mristudio-users-unsubscribe at mristudio.org
>  >
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.
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From susumu at mri.jhu.edu  Mon Apr 23 10:28:33 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 23 Apr 2012 10:28:33 -0400
Subject: [Mristudio-users] tractography problems
In-Reply-To: <1DC4211314F7D9458B66A28F947F60B9D44C9C903D@EXMBX4C.crha.bewell.ca>
References: <1DC4211314F7D9458B66A28F947F60B9D44C9C903D@EXMBX4C.crha.bewell.ca>
Message-ID: <CAEq9apKcXBCYRV+9RjDCJAfxAC6CgxxO9gdkfC=fV-HuGWnV6g@mail.gmail.com>

It seems that you have a problem with your gradient table.
Which scanner and gradient table are you using?

On Fri, Apr 20, 2012 at 4:19 PM, Jacquie Hodge <
Jacquie.Hodge at albertahealthservices.ca> wrote:

> Hello,
>
> I am having some difficulties and I'm not sure exactly what the problem
> is. I have attached a screen shot to show the ROI and the resulting fibers
> for CST that I get. The problem is I know there should be a full CST there.
> I have gone through the original images too see if there are any distorted
> ones to remove and they all look pretty clean. Do you have any suggestions
> as to what might be happening and how I can fix this?
>
> Also, I have drawn another ROI further up the tract and there are fibers
> there (this is not shown on the picture I am sending you).
>
> ANy help or suggestions is much appreciated as I do not want to lose this
> patient because of the scan!
>
> Thank you so much!
>
> Jacquie
>
> Jacquie Hodge MSc candidate in Neuroscience, BSc
> Neuroscience, University of Calgary
> Research Assistant, Calgary Pediatric Stroke Program
> Alberta Children's Hospital
> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
> Phone: 403-955-7733 Fax: 403-955-2922
> jacquie.hodge at albertahealthservices.ca
> Program website: www.perinatalstroke.com
> ________________________________________
> From: mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li [xli16 at jhmi.edu
> ]
> Sent: September 28, 2011 11:26 AM
> To: DTI Studio, ROI Editor,     DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
>
> You are welcome.
>
> The manuals and videos are at https://www.mristudio.org/wiki/user_manual
>
>
> Xin
>
> ----- Original Message -----
> From: uday bhaskar <udayanbhaskar at gmail.com>
> Date: Wednesday, September 28, 2011 12:57 pm
> Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
> To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <
> mristudio-users at mristudio.org>
>
>
> > Thank you.
> >
> >    Do you suggest some online tutorials for beginners.
> >
> >  --
> >  Thanks,
> >  Uday.
> >
> >  On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:
> >
> >  > Hello,
> >  >
> >  > It seems that you need to run vcredist_x64.exe on your computer
> > first. The
> >  > exe file is available at
> >  >
> >  > DtiStudio is a Microsoft Visual Studio applications. The Microsoft
> > Visual
> >  > Studio Redistribution package(vcredist_x64.exe) needs to be
> > installed on
> >  > your machine.
> >  >
> >  >
> >  > Xin
> >  >
> >  >
> >  > ----- Original Message -----
> >  > From: uday bhaskar <udayanbhaskar at gmail.com>
> >  > Date: Wednesday, September 28, 2011 12:45 pm
> >  > Subject: [Mristudio-users] Issues with Running DTI studio x64
> >  > To: mristudio-users at mristudio.org
> >  >
> >  >
> >  > > Hi,
> >  > >
> >  > >      I am a beginner and a new user of DTI studio. I am having a
> > problem
> >  > >  running the DTIstudio-latest-x64. When I try to run it gives me
> > an error
> >  > >  saying "The application failed to start because its
> >  > >  side-by-side configuration is incorrect".
> >  > >
> >  > >   Please let me know how to overcome this. Any help is appreciated.
> >  > >
> >  > >  --
> >  > >  Thanks,
> >  > >  Uday.
> >  > > _______________________________________________
> >  > >  mristudio-users mailing list
> >  > >  mristudio-users at mristudio.org
> >  > >
> >  > >  Unsubscribe, send a blank email to:
> >  > mristudio-users-unsubscribe at mristudio.org
> >  > _______________________________________________
> >  > mristudio-users mailing list
> >  > mristudio-users at mristudio.org
> >  >
> >  > Unsubscribe, send a blank email to:
> >  > mristudio-users-unsubscribe at mristudio.org
> >  >
> > _______________________________________________
> >  mristudio-users mailing list
> >  mristudio-users at mristudio.org
> >
> >  Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
> This message and any attached documents are only for the use of the
> intended recipient(s), are confidential and may contain privileged
> information. Any unauthorized review, use, retransmission, or other
> disclosure is strictly prohibited. If you have received this message in
> error, please notify the sender immediately, and then delete the original
> message. Thank you.
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From lwn_07 at yahoo.com.cn  Tue Apr 24 04:12:44 2012
From: lwn_07 at yahoo.com.cn (=?utf-8?B?5p2O5Y2r5aic?=)
Date: Tue, 24 Apr 2012 16:12:44 +0800 (CST)
Subject: [Mristudio-users] Question about fiber coordinate
Message-ID: <1335255164.37461.YahooMailClassic@web15605.mail.cnb.yahoo.com>

Dear mristudio users,
?
In FAQ page, it says fiber coordinate represents image matrix units. But the fiber data I read out have some mixed decimals' coordinate (eg:? x:54.00, y:38.78, z:1.62), is it right, shouldn't it be integers?? What does it mean? 
?
Another question is where is the origin of the coordinates? The fiber data shows 'xyzPtROI x:0, y:0, z:0', where is this PtROI?
?
Best regards,
?
Weina Li
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From yth0306 at yahoo.com.cn  Tue Apr 24 11:23:55 2012
From: yth0306 at yahoo.com.cn (Tianhua Yang)
Date: Tue, 24 Apr 2012 23:23:55 +0800 (CST)
Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgdHJhY3RvZ3JhcGh5IHBy?=
 =?utf-8?q?oblems?=
In-Reply-To: <CAEq9apKcXBCYRV+9RjDCJAfxAC6CgxxO9gdkfC=fV-HuGWnV6g@mail.gmail.com>
References: <1DC4211314F7D9458B66A28F947F60B9D44C9C903D@EXMBX4C.crha.bewell.ca>
	<CAEq9apKcXBCYRV+9RjDCJAfxAC6CgxxO9gdkfC=fV-HuGWnV6g@mail.gmail.com>
Message-ID: <1335281035.88525.YahooMailNeo@web15001.mail.cnb.yahoo.com>




???? susumu mori <susumu at mri.jhu.edu>
???? "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org> 
????? 2012?4?23?, ???, ?? 10:28
??: Re: [Mristudio-users] tractography problems


It seems that you have a problem with your gradient table. 
Which scanner and gradient table are you using?


On Fri, Apr 20, 2012 at 4:19 PM, Jacquie Hodge <Jacquie.Hodge at albertahealthservices.ca> wrote:

Hello,
>
>I am having some difficulties and I'm not sure exactly what the problem is. I have attached a screen shot to show the ROI and the resulting fibers for CST that I get. The problem is I know there should be a full CST there. I have gone through the original images too see if there are any distorted ones to remove and they all look pretty clean. Do you have any suggestions as to what might be happening and how I can fix this?
>
>Also, I have drawn another ROI further up the tract and there are fibers there (this is not shown on the picture I am sending you).
>
>ANy help or suggestions is much appreciated as I do not want to lose this patient because of the scan!
>
>Thank you so much!
>
>Jacquie
>
>Jacquie Hodge MSc candidate in Neuroscience, BSc
>Neuroscience, University of Calgary
>Research Assistant, Calgary Pediatric Stroke Program
>Alberta Children's Hospital
>2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>Phone: 403-955-7733 Fax: 403-955-2922
>jacquie.hodge at albertahealthservices.ca
>Program website: www.perinatalstroke.com
>________________________________________
>From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li [xli16 at jhmi.edu]
>Sent: September 28, 2011 11:26 AM
>To: DTI Studio, ROI Editor, ? ? DiffeoMap Questions/Support
>Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
>
>You are welcome.
>
>The manuals and videos are at https://www.mristudio.org/wiki/user_manual
>
>
>Xin
>
>----- Original Message -----
>From: uday bhaskar <udayanbhaskar at gmail.com>
>Date: Wednesday, September 28, 2011 12:57 pm
>Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
>To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>
>
>
>> Thank you.
>>
>> ? ?Do you suggest some online tutorials for beginners.
>>
>> ?--
>> ?Thanks,
>> ?Uday.
>>
>> ?On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:
>>
>> ?> Hello,
>> ?>
>> ?> It seems that you need to run vcredist_x64.exe on your computer
>> first. The
>> ?> exe file is available at
>> ?>
>> ?> DtiStudio is a Microsoft Visual Studio applications. The Microsoft
>> Visual
>> ?> Studio Redistribution package(vcredist_x64.exe) needs to be
>> installed on
>> ?> your machine.
>> ?>
>> ?>
>> ?> Xin
>> ?>
>> ?>
>> ?> ----- Original Message -----
>> ?> From: uday bhaskar <udayanbhaskar at gmail.com>
>> ?> Date: Wednesday, September 28, 2011 12:45 pm
>> ?> Subject: [Mristudio-users] Issues with Running DTI studio x64
>> ?> To: mristudio-users at mristudio.org
>> ?>
>> ?>
>> ?> > Hi,
>> ?> >
>> ?> > ? ? ?I am a beginner and a new user of DTI studio. I am having a
>> problem
>> ?> > ?running the DTIstudio-latest-x64. When I try to run it gives me
>> an error
>> ?> > ?saying "The application failed to start because its
>> ?> > ?side-by-side configuration is incorrect".
>> ?> >
>> ?> > ? Please let me know how to overcome this. Any help is appreciated.
>> ?> >
>> ?> > ?--
>> ?> > ?Thanks,
>> ?> > ?Uday.
>> ?> > _______________________________________________
>> ?> > ?mristudio-users mailing list
>> ?> > ?mristudio-users at mristudio.org
>> ?> >
>> ?> > ?Unsubscribe, send a blank email to:
>> ?> mristudio-users-unsubscribe at mristudio.org
>> ?> _______________________________________________
>> ?> mristudio-users mailing list
>> ?> mristudio-users at mristudio.org
>> ?>
>> ?> Unsubscribe, send a blank email to:
>> ?> mristudio-users-unsubscribe at mristudio.org
>> ?>
>> _______________________________________________
>> ?mristudio-users mailing list
>> ?mristudio-users at mristudio.org
>>
>> ?Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>
>This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.
>
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
>
>

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From susumu at mri.jhu.edu  Tue Apr 24 18:59:59 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 24 Apr 2012 18:59:59 -0400
Subject: [Mristudio-users] Question about fiber coordinate
In-Reply-To: <1335255164.37461.YahooMailClassic@web15605.mail.cnb.yahoo.com>
References: <1335255164.37461.YahooMailClassic@web15605.mail.cnb.yahoo.com>
Message-ID: <CAEq9apLMx4=O8qU4mkvST0QMZw6HTJPE1wheKzHNRQbco1peXQ@mail.gmail.com>

Hi Weina,

There are two types of data formats for fiber tracking. The "raw" format of
the fiber tracking is streamline information. For example, if you get 10
lines, you have 10 streamline information. Each streamline contains
information of sequential coordinates. These coordinates use floating point
coordinates as you saw. This is why streamline looks much more high
resolution than raw images. We artificially increase the resolution to draw
the streamlines. FAQ#1 describes how the streamline information is stored.
If you store your results as this streamline information, you can later
edit the results like removing some lines by the "NOT" operation.

The second format is the "image" format. In this format, the streamline
information is converted to a binary (1/0) masking image. If your image is
256x256x50, then this binary image also has 256x256x50. In this image,
pixels that contain the streamlines get "1" and others get "0". Once the
streamlines are converted to this binary image format, you can't edit
anymore.

I think Hangyi will explain what exactly is 'xyzPtROI'.

Susumu

On Tue, Apr 24, 2012 at 4:12 AM, ??? <lwn_07 at yahoo.com.cn> wrote:

> Dear mristudio users,
>
> In FAQ page, it says fiber coordinate represents image matrix units. But
> the fiber data I read out have some mixed decimals' coordinate (eg:
> x:54.00, y:38.78, z:1.62), is it right, shouldn't it be integers?  What
> does it mean?
>
> Another question is where is the origin of the coordinates? The fiber data
> shows 'xyzPtROI x:0, y:0, z:0', where is this PtROI?
>
> Best regards,
>
> Weina Li
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From lwn_07 at yahoo.com.cn  Tue Apr 24 21:53:55 2012
From: lwn_07 at yahoo.com.cn (=?utf-8?B?5p2O5Y2r5aic?=)
Date: Wed, 25 Apr 2012 09:53:55 +0800 (CST)
Subject: [Mristudio-users] Question about fiber coordinate
In-Reply-To: <CAEq9apLMx4=O8qU4mkvST0QMZw6HTJPE1wheKzHNRQbco1peXQ@mail.gmail.com>
Message-ID: <1335318835.95170.YahooMailClassic@web15608.mail.cnb.yahoo.com>

Thanks susumu! Thanks Hangyi!
Best regards.
?
Weina
2012-4-25

--- 12?4?25????, susumu mori <susumu at mri.jhu.edu> ???


???: susumu mori <susumu at mri.jhu.edu>
??: Re: [Mristudio-users] Question about fiber coordinate
???: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>, "Hangyi Jiang" <hjiang at jhmi.edu>
??: 2012?4?25?,??,??6:59



Hi Weina,


There are two types of data formats for fiber tracking. The "raw" format of the fiber tracking is streamline information. For example, if you get 10 lines, you have 10 streamline information. Each streamline contains information of sequential coordinates. These coordinates use floating point coordinates as you saw. This is why streamline looks much more high resolution than raw images. We artificially increase the resolution to draw the streamlines. FAQ#1 describes how the streamline information is stored. If you store your results as this streamline information, you can later edit the results like removing some lines by the "NOT"?operation.


The second format is the "image" format. In this format, the streamline information is converted to a binary (1/0) masking image. If your image is 256x256x50, then this binary image also has 256x256x50. In this image, pixels that contain the streamlines get "1" and others get "0". Once the streamlines are converted to this binary image format, you can't edit anymore.

I think Hangyi will explain what exactly is 'xyzPtROI'.


Susumu


On Tue, Apr 24, 2012 at 4:12 AM, ??? <lwn_07 at yahoo.com.cn> wrote:






Dear mristudio users,
?
In FAQ page, it says fiber coordinate represents image matrix units. But the fiber data I read out have some mixed decimals' coordinate (eg:? x:54.00, y:38.78, z:1.62), is it right, shouldn't it be integers?? What does it mean? 
?
Another question is where is the origin of the coordinates? The fiber data shows 'xyzPtROI x:0, y:0, z:0', where is this PtROI?
?
Best regards,
?
Weina Li
_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org



-----???????-----


_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
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From farshidfar at sums.ac.ir  Tue May  1 16:32:12 2012
From: farshidfar at sums.ac.ir (farshidfar at sums.ac.ir)
Date: Wed, 02 May 2012 01:02:12 +0430
Subject: [Mristudio-users] fiber tracking and ROI drawing problem
Message-ID: <8a272038b4c64f35ac7cdb63a46d199f.squirrel@mail.sums.ac.ir>

Hello
I'm a new DTI Studio user.I have three problems.Could you please help me
to solve them?
1)I did fiber tracking step by step as it's been explained in DTI Studio
manual;The fiber tab is showed in the lower-right corner of menu bar,but
when I want to save them,it showes an error(There is no fiber to save) and
there isn't also any fiber file in pull down menu in image tab and only
show color map.0 in primary image view window.
2)when I want to load two files(anatomy and color map)at the same time
with ROI editor,it showes an error(the image you want to load must be the
same dimensions and orientation as the other images in the image list)
3)After drawing ROIs on color map image in ROI editor,I don't know  where
and  how I can assign different numbers to them and create word image
file.Could you please send me a sample of image tract file and word image
file for overlaying.
                                                   sincerly


-----------------------------------------
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From abeer.hani at duke.edu  Tue May  1 16:35:17 2012
From: abeer.hani at duke.edu (Dr Abeer Hani)
Date: Tue, 01 May 2012 20:35:17 +0000
Subject: [Mristudio-users] fiber tracking and ROI drawing problem
In-Reply-To: <8a272038b4c64f35ac7cdb63a46d199f.squirrel@mail.sums.ac.ir>
References: <8a272038b4c64f35ac7cdb63a46d199f.squirrel@mail.sums.ac.ir>
Message-ID: <AB27B57D-748E-4806-8B21-9F6D2892EED3@duke.edu>

Sorry, I am trying to learn mristudio just now. I am sorry I cannot help because I do not understand what you are asking.
Best,
Abeer


On May 1, 2012, at 4:32 PM, "farshidfar at sums.ac.ir" <farshidfar at sums.ac.ir> wrote:

> Hello
> I'm a new DTI Studio user.I have three problems.Could you please help me
> to solve them?
> 1)I did fiber tracking step by step as it's been explained in DTI Studio
> manual;The fiber tab is showed in the lower-right corner of menu bar,but
> when I want to save them,it showes an error(There is no fiber to save) and
> there isn't also any fiber file in pull down menu in image tab and only
> show color map.0 in primary image view window.
> 2)when I want to load two files(anatomy and color map)at the same time
> with ROI editor,it showes an error(the image you want to load must be the
> same dimensions and orientation as the other images in the image list)
> 3)After drawing ROIs on color map image in ROI editor,I don't know  where
> and  how I can assign different numbers to them and create word image
> file.Could you please send me a sample of image tract file and word image
> file for overlaying.
>                                                   sincerly
> 
> 
> -----------------------------------------
> This email was sent using SquirrelMail.
>   "Webmail for nuts!"
> http://squirrelmail.org/
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org


From xli16 at jhmi.edu  Tue May  1 17:22:11 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Tue, 01 May 2012 17:22:11 -0400
Subject: [Mristudio-users] fiber tracking and ROI drawing problem
In-Reply-To: <8a272038b4c64f35ac7cdb63a46d199f.squirrel@mail.sums.ac.ir>
References: <8a272038b4c64f35ac7cdb63a46d199f.squirrel@mail.sums.ac.ir>
Message-ID: <70b0cd2824b4f.4fa01bc3@johnshopkins.edu>

Hello,

ROIEditor requires that all images to be loaded must have same size and same orientation. Please check if the images you want to load have the same parameters.


After you draw a ROI, you can add it to an ROI object by clicking ?add? under the SELECTION menu. After you create some ROI objects, you can save them as a word image file by clicking on the file save button found under the ROI menu.


Please take a look at this online manual https://www.mristudio.org/wiki/user_manual/roieditor/ROIDraw_Load_Save


Xin




----- Original Message -----
From: farshidfar at sums.ac.ir
Date: Tuesday, May 1, 2012 4:32 pm
Subject: [Mristudio-users] fiber tracking and ROI drawing problem
To: mristudio-users at mristudio.org


> Hello
>  I'm a new DTI Studio user.I have three problems.Could you please help 
> me
>  to solve them?
>  1)I did fiber tracking step by step as it's been explained in DTI Studio
>  manual;The fiber tab is showed in the lower-right corner of menu bar,but
>  when I want to save them,it showes an error(There is no fiber to 
> save) and
>  there isn't also any fiber file in pull down menu in image tab and only
>  show color map.0 in primary image view window.
>  2)when I want to load two files(anatomy and color map)at the same time
>  with ROI editor,it showes an error(the image you want to load must be 
> the
>  same dimensions and orientation as the other images in the image list)
>  3)After drawing ROIs on color map image in ROI editor,I don't know  where
>  and  how I can assign different numbers to them and create word image
>  file.Could you please send me a sample of image tract file and word image
>  file for overlaying.
>                                                     sincerly
>  
>  
>  -----------------------------------------
>  This email was sent using SquirrelMail.
>     "Webmail for nuts!"
>  
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 


From farshidfar at sums.ac.ir  Tue May  1 17:33:05 2012
From: farshidfar at sums.ac.ir (farshidfar at sums.ac.ir)
Date: Wed, 02 May 2012 02:03:05 +0430
Subject: [Mristudio-users] tractography problems
In-Reply-To: <CAEq9apKcXBCYRV+9RjDCJAfxAC6CgxxO9gdkfC=fV-HuGWnV6g@mail.gmail.com>
References: <1DC4211314F7D9458B66A28F947F60B9D44C9C903D@EXMBX4C.crha.bewell.ca>
	<CAEq9apKcXBCYRV+9RjDCJAfxAC6CgxxO9gdkfC=fV-HuGWnV6g@mail.gmail.com>
Message-ID: <cf38379c112b0a05506c1e1f45124c5d.squirrel@mail.sums.ac.ir>


 Thanks for your  answer. my scanner is siemens 1.5 Tesla with 20 gradient
directions and I used predefined gradient table in DTI studio software.
> It seems that you have a problem with your gradient table.
> Which scanner and gradient table are you using?
>
> On Fri, Apr 20, 2012 at 4:19 PM, Jacquie Hodge <
> Jacquie.Hodge at albertahealthservices.ca> wrote:
>
>> Hello,
>>
>> I am having some difficulties and I'm not sure exactly what the problem
>> is. I have attached a screen shot to show the ROI and the resulting
>> fibers
>> for CST that I get. The problem is I know there should be a full CST
>> there.
>> I have gone through the original images too see if there are any
>> distorted
>> ones to remove and they all look pretty clean. Do you have any
>> suggestions
>> as to what might be happening and how I can fix this?
>>
>> Also, I have drawn another ROI further up the tract and there are fibers
>> there (this is not shown on the picture I am sending you).
>>
>> ANy help or suggestions is much appreciated as I do not want to lose
>> this
>> patient because of the scan!
>>
>> Thank you so much!
>>
>> Jacquie
>>
>> Jacquie Hodge MSc candidate in Neuroscience, BSc
>> Neuroscience, University of Calgary
>> Research Assistant, Calgary Pediatric Stroke Program
>> Alberta Children's Hospital
>> 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8
>> Phone: 403-955-7733 Fax: 403-955-2922
>> jacquie.hodge at albertahealthservices.ca
>> Program website: www.perinatalstroke.com
>> ________________________________________
>> From: mristudio-users-bounces at mristudio.org [
>> mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li
>> [xli16 at jhmi.edu
>> ]
>> Sent: September 28, 2011 11:26 AM
>> To: DTI Studio, ROI Editor,     DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
>>
>> You are welcome.
>>
>> The manuals and videos are at https://www.mristudio.org/wiki/user_manual
>>
>>
>> Xin
>>
>> ----- Original Message -----
>> From: uday bhaskar <udayanbhaskar at gmail.com>
>> Date: Wednesday, September 28, 2011 12:57 pm
>> Subject: Re: [Mristudio-users] Issues with Running DTI studio x64
>> To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <
>> mristudio-users at mristudio.org>
>>
>>
>> > Thank you.
>> >
>> >    Do you suggest some online tutorials for beginners.
>> >
>> >  --
>> >  Thanks,
>> >  Uday.
>> >
>> >  On Wed, Sep 28, 2011 at 12:51 PM, Xin Li <xli16 at jhmi.edu> wrote:
>> >
>> >  > Hello,
>> >  >
>> >  > It seems that you need to run vcredist_x64.exe on your computer
>> > first. The
>> >  > exe file is available at
>> >  >
>> >  > DtiStudio is a Microsoft Visual Studio applications. The Microsoft
>> > Visual
>> >  > Studio Redistribution package(vcredist_x64.exe) needs to be
>> > installed on
>> >  > your machine.
>> >  >
>> >  >
>> >  > Xin
>> >  >
>> >  >
>> >  > ----- Original Message -----
>> >  > From: uday bhaskar <udayanbhaskar at gmail.com>
>> >  > Date: Wednesday, September 28, 2011 12:45 pm
>> >  > Subject: [Mristudio-users] Issues with Running DTI studio x64
>> >  > To: mristudio-users at mristudio.org
>> >  >
>> >  >
>> >  > > Hi,
>> >  > >
>> >  > >      I am a beginner and a new user of DTI studio. I am having a
>> > problem
>> >  > >  running the DTIstudio-latest-x64. When I try to run it gives me
>> > an error
>> >  > >  saying "The application failed to start because its
>> >  > >  side-by-side configuration is incorrect".
>> >  > >
>> >  > >   Please let me know how to overcome this. Any help is
>> appreciated.
>> >  > >
>> >  > >  --
>> >  > >  Thanks,
>> >  > >  Uday.
>> >  > > _______________________________________________
>> >  > >  mristudio-users mailing list
>> >  > >  mristudio-users at mristudio.org
>> >  > >
>> >  > >  Unsubscribe, send a blank email to:
>> >  > mristudio-users-unsubscribe at mristudio.org
>> >  > _______________________________________________
>> >  > mristudio-users mailing list
>> >  > mristudio-users at mristudio.org
>> >  >
>> >  > Unsubscribe, send a blank email to:
>> >  > mristudio-users-unsubscribe at mristudio.org
>> >  >
>> > _______________________________________________
>> >  mristudio-users mailing list
>> >  mristudio-users at mristudio.org
>> >
>> >  Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>> This message and any attached documents are only for the use of the
>> intended recipient(s), are confidential and may contain privileged
>> information. Any unauthorized review, use, retransmission, or other
>> disclosure is strictly prohibited. If you have received this message in
>> error, please notify the sender immediately, and then delete the
>> original
>> message. Thank you.
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



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From rajagov2 at ccf.org  Thu May  3 12:00:02 2012
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Thu, 03 May 2012 12:00:02 -0400
Subject: [Mristudio-users] Superimposing two tracts
Message-ID: <190A50FE6C374841B0D466F13F96987C0AF938@CCHSCLEXMB80.cc.ad.cchs.net>

Dear All,
 
I reconstructed CST originating from motor cortex and CST from sensory cortex. For mauscript figure preparation I would like to overlay these tracts one over the other in different colors how to do this using DTI studio or ROI editor or other MRI studio softwares
 
Thanks
Venkat

===================================

 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News & World Report (2010).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy.  Thank you.
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From susumu at mri.jhu.edu  Thu May  3 14:30:35 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 03 May 2012 14:30:35 -0400
Subject: [Mristudio-users] Superimposing two tracts
In-Reply-To: <190A50FE6C374841B0D466F13F96987C0AF938@CCHSCLEXMB80.cc.ad.cchs.net>
References: <190A50FE6C374841B0D466F13F96987C0AF938@CCHSCLEXMB80.cc.ad.cchs.net>
Message-ID: <CAEq9apKv3NYMSFLCazX+=pxc+gPt89TEAnAsuPEAkoPiC7y7zw@mail.gmail.com>

If you want to show multiple tractrography results, you first need to
save the tractography results with different colors in separated files
using DtiStudio format. Then load them. When you load the second and
subsequent files, you need to specify that you don't want to erase the
fibers which are already loaded.

On Thu, May 3, 2012 at 12:00 PM, Rajagopalan, Venkateswaran
<rajagov2 at ccf.org> wrote:
> Dear All,
>
> I reconstructed CST originating from motor cortex and CST from sensory
> cortex. For mauscript figure preparation I would like to overlay these
> tracts one over the other in different colors how to do this using DTI
> studio or ROI editor or other MRI studio softwares
>
> Thanks
> Venkat
>
> ===================================
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2010).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>

From jimhard at 163.com  Fri May  4 01:11:52 2012
From: jimhard at 163.com (xhh)
Date: Fri, 04 May 2012 13:11:52 +0800 (CST)
Subject: [Mristudio-users] About muscle fiber
Message-ID: <6a40a8a0.177ff.1371642e5c3.Coremail.jimhard$163.com@jhuin3.jhu.edu>

Dear MRIStudio users,


I want to show the  muscle fibers,such as tongue and soft palate, whether it is suitable to use DTIstudio. If not,  is there avaible software ? Thanks a lot.     






Jim
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From rsutter3 at jhmi.edu  Fri May  4 05:45:58 2012
From: rsutter3 at jhmi.edu (Raoul Sutter)
Date: Fri, 04 May 2012 05:45:58 -0400
Subject: [Mristudio-users] (no subject)
In-Reply-To: <6a40a8a0.177ff.1371642e5c3.Coremail.jimhard$163.com@jhuin3.jhu.edu>
References: <6a40a8a0.177ff.1371642e5c3.Coremail.jimhard$163.com@jhuin3.jhu.edu>
Message-ID: <7230bb322654b.4fa36d16@johnshopkins.edu>



From susumu at mri.jhu.edu  Fri May  4 06:02:31 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 04 May 2012 06:02:31 -0400
Subject: [Mristudio-users] About muscle fiber
In-Reply-To: <6a40a8a0.177ff.1371642e5c3.Coremail.jimhard$163.com@jhuin3.jhu.edu>
References: <6a40a8a0.177ff.1371642e5c3.Coremail.jimhard$163.com@jhuin3.jhu.edu>
Message-ID: <CAEq9ap+Cz0uVdkwsa+d=UHUbotuvbt+rMC9AKJ9etc+QAQ71_g@mail.gmail.com>

As long as you have a DTI dataset, acquired by a MRI scanner, you can
use DtiStudio, no matter which part of the body is imaged. However,
practically, tongue imaging is not as easy as the brain because it is
difficult to keep it still. During a long DTI scan, it has to be stay
still.

On Fri, May 4, 2012 at 1:11 AM, xhh <jimhard at 163.com> wrote:
> Dear MRIStudio users,
>
> I want to show the ?muscle fibers,such as tongue and soft palate, whether it
> is suitable to use DTIstudio. If not, ?is there avaible software ? Thanks a
> lot.
>
>
>
> Jim
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>


From Reid.Robert at mayo.edu  Wed May  9 18:09:18 2012
From: Reid.Robert at mayo.edu (Reid, Robert I. (Rob))
Date: Wed, 09 May 2012 17:09:18 -0500
Subject: [Mristudio-users] How does DTI-Studio fit tensors?
Message-ID: <A1E20700996E994AA3F26938904208E101B7BCF0@msgebe10.mfad.mfroot.org>

Hello,

When fitting tensors, does DTI-Studio do any averaging or weighting with
neighboring voxels?  Or rejection of outlier DWIs?  I noticed that
unlike FSL's dtifit it does not produce any fractional anisotropies > 1,
but I would like to know what it is doing to enforce that.

Thanks,

     Rob

-- 
Rob Reid
Sr. Analyst/Programmer, 
Aging and Dementia Imaging Research
Opus Center for Advanced Imaging Research
Mayo Clinic
200 First Street SW
Rochester, MN 55905
http://www.mayoclinic.org

From fatemeh.derakhshan at gmail.com  Fri May 11 13:27:32 2012
From: fatemeh.derakhshan at gmail.com (Fatemeh Derakhshan)
Date: Fri, 11 May 2012 12:27:32 -0500
Subject: [Mristudio-users] Is there an exact correlation between FA value
	and total tract fibers ?
Message-ID: <CAJhfb4zuzni5_y23jk0QjcrDM8NqzKCnV_BKVn8M6Qfqxrx0hQ@mail.gmail.com>

Hi all,
I'm working on DTI images of mice; recently I found out that in some of my
transgenic mouse brains the total tract fibers were lower than normal in
corpus callosum,while FA values are within the normal ranges. We use
ROI approach to detect tract fiber numbers. Does it at all make sense?
Thanks

-- 
Fatemeh Derakhshan
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From fatemeh.derakhshan at gmail.com  Fri May 11 13:28:53 2012
From: fatemeh.derakhshan at gmail.com (Fatemeh Derakhshan)
Date: Fri, 11 May 2012 12:28:53 -0500
Subject: [Mristudio-users] Is there an exact correlation between FA value
	and total tract fibers ?
Message-ID: <CAJhfb4z9e4_MPJN3hHdwsc9Wzd0MZ+yjBPZJA-6HcYOiro+5Xg@mail.gmail.com>

Hi all,
I'm working on DTI images of mice; recently I found out that in some of my
transgenic mouse brains the total tract fibers were lower than normal in
corpus callosum,while FA values are within the normal ranges. We use
ROI approach to detect tract fiber numbers. Does it at all make sense?
Thanks

On Thu, May 3, 2012 at 1:30 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> If you want to show multiple tractrography results, you first need to
> save the tractography results with different colors in separated files
> using DtiStudio format. Then load them. When you load the second and
> subsequent files, you need to specify that you don't want to erase the
> fibers which are already loaded.
>
> On Thu, May 3, 2012 at 12:00 PM, Rajagopalan, Venkateswaran
> <rajagov2 at ccf.org> wrote:
> > Dear All,
> >
> > I reconstructed CST originating from motor cortex and CST from sensory
> > cortex. For mauscript figure preparation I would like to overlay these
> > tracts one over the other in different colors how to do this using DTI
> > studio or ROI editor or other MRI studio softwares
> >
> > Thanks
> > Venkat
> >
> > ===================================
> >
> >  Please consider the environment before printing this e-mail
> >
> > Cleveland Clinic is ranked one of the top hospitals
> > in America by U.S.News & World Report (2010).
> > Visit us online at http://www.clevelandclinic.org for
> > a complete listing of our services, staff and
> > locations.
> >
> >
> > Confidentiality Note:  This message is intended for use
> > only by the individual or entity to which it is addressed
> > and may contain information that is privileged,
> > confidential, and exempt from disclosure under applicable
> > law.  If the reader of this message is not the intended
> > recipient or the employee or agent responsible for
> > delivering the message to the intended recipient, you are
> > hereby notified that any dissemination, distribution or
> > copying of this communication is strictly prohibited.  If
> > you have received this communication in error,  please
> > contact the sender immediately and destroy the material in
> > its entirety, whether electronic or hard copy.  Thank you.
> >
> >
> > _______________________________________________
> > mristudio-users mailing list
> > mristudio-users at mristudio.org
> > http://lists.mristudio.org/mailman/listinfo/
> > Unsubscribe, send a blank email to:
> > mristudio-users-unsubscribe at mristudio.org
> >
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



-- 
Fatemeh Derakhshan
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From sychrbust at 163.com  Sat May 12 09:26:19 2012
From: sychrbust at 163.com (sychrbust)
Date: Sat, 12 May 2012 21:26:19 +0800 (CST)
Subject: [Mristudio-users] Question:File size is bigger than DW-image size
Message-ID: <376568a0.2bfe9.137413a76e8.Coremail.sychrbust@163.com>

Hi,all
When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?".
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From yth0306 at yahoo.com.cn  Sat May 12 21:06:40 2012
From: yth0306 at yahoo.com.cn (Tianhua Yang)
Date: Sun, 13 May 2012 09:06:40 +0800 (CST)
Subject: [Mristudio-users] =?gb2312?b?ILvYuLSjuiAgUXVlc3Rpb246RmlsZSBzaXpl?=
 =?gb2312?b?IGlzIGJpZ2dlciB0aGFuIERXLWltYWdlIHNpemU=?=
In-Reply-To: <376568a0.2bfe9.137413a76e8.Coremail.sychrbust@163.com>
References: <376568a0.2bfe9.137413a76e8.Coremail.sychrbust@163.com>
Message-ID: <1336871200.99323.YahooMailNeo@web15003.mail.cnb.yahoo.com>




???? sychrbust <sychrbust at 163.com>
???? mristudio-users at mristudio.org 
????? 2012?5?12?, ???, ?? 9:26
??: [Mristudio-users] Question:File size is bigger than DW-image size


Hi,all
When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?". 


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From rajagov2 at ccf.org  Mon May 14 12:20:00 2012
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Mon, 14 May 2012 12:20:00 -0400
Subject: [Mristudio-users] Spherical index
Message-ID: <190A50FE6C374841B0D466F13F96987C0AF981@CCHSCLEXMB80.cc.ad.cchs.net>

Hi All,
 
I would like to study spherical index CS changes between my control and patients. Unfortunately I forgot to save the CS.dat file when I initially ran (tensor fit and other DTI processing steps). I wondering without going through all the steps of feeding my grad table and running all the tensor calculations I am wondering is it possible to calculate CS measure using Eigen values (since these files are automatically saved ). Or if you can tell the the formula to calculate CS measure which is used in DTI studio (I understand from Westin's paper he showed one can used 3 different normalizationprocedures one is to use, maximum diffusivity eigen value 1,  trace, or norm of the tensor so which one did DTI studio used).
 
Thanks
Venkat

===================================

 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
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Visit us online at http://www.clevelandclinic.org for
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Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
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From kbekaath at yahoo.gr  Mon May 14 13:13:06 2012
From: kbekaath at yahoo.gr (=?iso-8859-7?B?6uH05fHp7eEg7PDl6uE=?=)
Date: Mon, 14 May 2012 18:13:06 +0100 (BST)
Subject: [Mristudio-users] questions about DTI studio
Message-ID: <1337015586.75595.YahooMailNeo@web171606.mail.ir2.yahoo.com>

Dear Proffesor,
I am a new colleague trying to use DTI studio and?I have some problems in creating fiber tracking.??I am using Dicom raw data. I start by choosing DTI mapping and clicking the Siemns-GE-Phillps DICOM. Then?I select the predifined Johns -30 gradient and open a folder with either a simple MRI or a DTI MRI sequence. My next step is defining the ROI but afterwards?I am unable to find the button?that would create the fiber tracking images. I would apprecate your?help in pointing out to me my mistakes and tp guide me in the correct way of using your program. 
Thank you for your time.
?
Katerina Beka MD, M.Sc.
Radiology specialist.
Athens, Greece
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From susumu at mri.jhu.edu  Tue May 15 01:41:47 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 15 May 2012 01:41:47 -0400
Subject: [Mristudio-users] Spherical index
In-Reply-To: <190A50FE6C374841B0D466F13F96987C0AF981@CCHSCLEXMB80.cc.ad.cchs.net>
References: <Ac0x7WlxPnzcJZ4KSp2aVmkd4pTXjg==@jhmin1.jhmi.edu>
	<190A50FE6C374841B0D466F13F96987C0AF981@CCHSCLEXMB80.cc.ad.cchs.net>
Message-ID: <CAEq9apKDGkf86KVR76eJEsS54j5v6T=M38H3uJHi05XE-PypxQ@mail.gmail.com>

Hi Vankat,

If you still have three eigenvalues, you can calculate CS using Excel.
I believe Cs is simply lambda3/lambda1, but please check Westin's
original paper to make sure.

Susumu

On Mon, May 14, 2012 at 12:20 PM, Rajagopalan, Venkateswaran
<rajagov2 at ccf.org> wrote:
> Hi All,
>
> I would like to study spherical index CS changes between my control and
> patients. Unfortunately I forgot to save the CS.dat file when I initially
> ran (tensor fit and other DTI processing steps). I wondering without going
> through all the steps of feeding my grad table and running all the tensor
> calculations I am wondering is it possible to calculate CS measure using
> Eigen values (since these files?are automatically saved ). Or if you can
> tell the the formula to calculate CS measure which is used in DTI studio (I
> understand from Westin's paper he?showed one can used?3 different
> normalizationprocedures one is to use, maximum diffusivity eigen value 1,
> ?trace, or norm of the tensor so which one did DTI studio used).
>
> Thanks
> Venkat
>
> ===================================
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News & World Report (2010).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>


From sychrbust at 163.com  Tue May 15 07:44:57 2012
From: sychrbust at 163.com (sychrbust)
Date: Tue, 15 May 2012 19:44:57 +0800 (CST)
Subject: [Mristudio-users] ''File size is bigger than DW-image size,
	continue anyway''  .
Message-ID: <2c5fbbc8.14797.1375050bca4.Coremail.sychrbust@163.com>

 
????????????????????????????????????????????????????????????
 
 ??????????
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From susumu at mri.jhu.edu  Tue May 15 09:59:36 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 15 May 2012 09:59:36 -0400
Subject: [Mristudio-users] Is there an exact correlation between FA
 value and total tract fibers ?
In-Reply-To: <CAJhfb4zuzni5_y23jk0QjcrDM8NqzKCnV_BKVn8M6Qfqxrx0hQ@mail.gmail.com>
References: <CAJhfb4zuzni5_y23jk0QjcrDM8NqzKCnV_BKVn8M6Qfqxrx0hQ@mail.gmail.com>
Message-ID: <CAEq9apKv4iY180-LPMmM_7LAQt9buKVd7f8phqFMusVj+tnXFA@mail.gmail.com>

It can happen when white matter becomes smaller while FA doesn't
change a lot. This would be the most natural interpretation.
Also, tractography could be relatively insensitive to decreased FA
because tractography tends to extract only the core of the tract with
high FA.

Also, if there is one area along the tract where a portion of the
tract has lower FA, tractography stops when it hits the low FA area
due to the FA threshold. This also would lead to smaller tractography
with unchanged FA.

So, there are several possibilities.

On Fri, May 11, 2012 at 1:27 PM, Fatemeh Derakhshan
<fatemeh.derakhshan at gmail.com> wrote:
>
> Hi all,
> I'm working on DTI images of mice; recently I found out that in some of my
> transgenic mouse brains the?total tract fibers were lower than normal in
> corpus callosum,while FA values are within the normal ranges. We use
> ROI?approach?to detect tract fiber numbers. Does it at all make sense?
> Thanks
>
> --
> Fatemeh Derakhshan
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>


From susumu at mri.jhu.edu  Tue May 15 21:37:40 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 15 May 2012 21:37:40 -0400
Subject: [Mristudio-users] How does DTI-Studio fit tensors?
In-Reply-To: <A1E20700996E994AA3F26938904208E101B7BCF0@msgebe10.mfad.mfroot.org>
References: <Ac0uMGDd0JCIHZoVS9+XiZUVmL8KIw==@jhmin1.jhmi.edu>
	<A1E20700996E994AA3F26938904208E101B7BCF0@msgebe10.mfad.mfroot.org>
Message-ID: <CAEq9apJufFcE406C74JS7bWzoHFg9QX9fmRTE43nOHms_Xphzw@mail.gmail.com>

Hi Rob,

I think Hangyi can give you information about how we avoid FA>1.

We are offering outlier rejection in the latest version, either by a
slice-by-slice or pixel-by-pixel approach.

Susumu

On Wed, May 9, 2012 at 6:09 PM, Reid, Robert I. (Rob)
<Reid.Robert at mayo.edu> wrote:
> Hello,
>
> When fitting tensors, does DTI-Studio do any averaging or weighting with
> neighboring voxels? ?Or rejection of outlier DWIs? ?I noticed that
> unlike FSL's dtifit it does not produce any fractional anisotropies > 1,
> but I would like to know what it is doing to enforce that.
>
> Thanks,
>
> ? ? Rob
>
> --
> Rob Reid
> Sr. Analyst/Programmer,
> Aging and Dementia Imaging Research
> Opus Center for Advanced Imaging Research
> Mayo Clinic
> 200 First Street SW
> Rochester, MN 55905
> http://www.mayoclinic.org
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org


From amirzolal at gmail.com  Sun May 20 09:38:27 2012
From: amirzolal at gmail.com (Amir Zolal)
Date: Sun, 20 May 2012 15:38:27 +0200
Subject: [Mristudio-users] probabilistic tractography for windows
Message-ID: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>

Hello,

this is slightly off-topic, but is there any user-friendly probabilistic
tractography software *for windows* that you have used or know of? I want
to compare the deterministic tracking technique with the probabilistic, but
I cannot run FSL at work at this time and I haven't found any real
alternative for windows.

Thanks in advance,

Amir Zolal
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From lujiaoluo1990 at 126.com  Sun May 20 09:50:27 2012
From: lujiaoluo1990 at 126.com (=?GBK?B?wt7otL2/?=)
Date: Sun, 20 May 2012 21:50:27 +0800 (CST)
Subject: [Mristudio-users] probabilistic tractography for windows
In-Reply-To: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
References: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
Message-ID: <73de15dc.100a5.1376a836f35.Coremail.lujiaoluo1990@126.com>


hello? I really want to help, but I am a newer in this mri field, so I haven't used any other probabilistic tractography  software for windows. I am sorry that I can't offer any help.

 


At 2012-05-20 21:38:27,"Amir Zolal" <amirzolal at gmail.com> wrote:
Hello,


this is slightly off-topic, but is there any user-friendly probabilistic tractography software *for windows* that you have used or know of? I want to compare the deterministic tracking technique with the probabilistic, but I cannot run FSL at work at this time and I haven't found any real alternative for windows.


Thanks in advance,


Amir Zolal
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From susumu at mri.jhu.edu  Sun May 20 10:32:10 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 20 May 2012 10:32:10 -0400
Subject: [Mristudio-users] probabilistic tractography for windows
In-Reply-To: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
References: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
Message-ID: <CAEq9apKJML6hHSrqhguqMDfs3CF3fQh999Y4rc1UHzxy=i5NQA@mail.gmail.com>

We are working on it. Hopefully we can deliver it this year.....

On Sun, May 20, 2012 at 9:38 AM, Amir Zolal <amirzolal at gmail.com> wrote:
> Hello,
>
> this is slightly off-topic, but is there any user-friendly probabilistic
> tractography software *for windows* that you have used or know of? I want to
> compare the deterministic tracking technique with the probabilistic, but I
> cannot run FSL at work at this time and I haven't found any real alternative
> for windows.
>
> Thanks in advance,
>
> Amir Zolal
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>

From syc2007.happy at 163.com  Tue May  8 22:33:16 2012
From: syc2007.happy at 163.com (syc2007.happy)
Date: Wed, 09 May 2012 02:33:16 -0000
Subject: [Mristudio-users] How to know the number of DTI voxel size?
Message-ID: <59227547.ac19.1372f71674f.Coremail.syc2007.happy@163.com>


 
I download DTI data from MRI Studio, I have the difficult  looking for the parameter of voxel size.


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From ssgao at qq.com  Thu May 24 23:38:01 2012
From: ssgao at qq.com (=?ISO-8859-1?B?c3NnYW8=?=)
Date: Fri, 25 May 2012 11:38:01 +0800
Subject: [Mristudio-users] How does DTI-Studio fit tensors?
Message-ID: <tencent_7FA3289C04456D971651B290@qq.com>

Hi everyone,
  
 Please find the dcm file in the attachement.
  
 All slices were store in one dcm file. How to divide them into slice by slice. I want to analysis one slice.
   
  
 Cliff Gao

 

 ------------------ Original ------------------
  From:  "susumu mori"<susumu at mri.jhu.edu>;
 Date:  Wed, May 16, 2012 09:37 AM
 To:  "DTI Studio, ROI Editor, DiffeoMap Questions/Support"<mristudio-users at mristudio.org>; "Hangyi Jiang"<hjiang at jhmi.edu>; 
 
 Subject:  Re: [Mristudio-users] How does DTI-Studio fit tensors?

 

Hi Rob,

I think Hangyi can give you information about how we avoid FA>1.

We are offering outlier rejection in the latest version, either by a
slice-by-slice or pixel-by-pixel approach.

Susumu

On Wed, May 9, 2012 at 6:09 PM, Reid, Robert I. (Rob)
<Reid.Robert at mayo.edu> wrote:
> Hello,
>
> When fitting tensors, does DTI-Studio do any averaging or weighting with
> neighboring voxels?  Or rejection of outlier DWIs?  I noticed that
> unlike FSL's dtifit it does not produce any fractional anisotropies > 1,
> but I would like to know what it is doing to enforce that.
>
> Thanks,
>
>     Rob
>
> --
> Rob Reid
> Sr. Analyst/Programmer,
> Aging and Dementia Imaging Research
> Opus Center for Advanced Imaging Research
> Mayo Clinic
> 200 First Street SW
> Rochester, MN 55905
> http://www.mayoclinic.org
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org

_______________________________________________
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mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From ycq0565 at 126.com  Wed May 30 05:14:36 2012
From: ycq0565 at 126.com (ycq0565)
Date: Wed, 30 May 2012 17:14:36 +0800 (CST)
Subject: [Mristudio-users] How can I get the MD map?
In-Reply-To: <CAEq9apKJML6hHSrqhguqMDfs3CF3fQh999Y4rc1UHzxy=i5NQA@mail.gmail.com>
References: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
	<CAEq9apKJML6hHSrqhguqMDfs3CF3fQh999Y4rc1UHzxy=i5NQA@mail.gmail.com>
Message-ID: <7a7ad6fe.188cc.1379d067bc1.Coremail.ycq0565@126.com>

hi everybody,
I am a new DTIstudio user,and I need to get the MD map from DTIstudio,if anyone can help?
thanks a lot,and best wishes.
Dr.Ye--

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From susumu at mri.jhu.edu  Wed May 30 09:48:36 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 30 May 2012 09:48:36 -0400
Subject: [Mristudio-users] How can I get the MD map?
In-Reply-To: <7a7ad6fe.188cc.1379d067bc1.Coremail.ycq0565@126.com>
References: <CADZNnOm5RbznL6fMUdmSnXVSTWfWLeKDD+Sy9bgJjAT3co7rpg@mail.gmail.com>
	<CAEq9apKJML6hHSrqhguqMDfs3CF3fQh999Y4rc1UHzxy=i5NQA@mail.gmail.com>
	<7a7ad6fe.188cc.1379d067bc1.Coremail.ycq0565@126.com>
Message-ID: <CAEq9apJ6bHSTE54k=2C+wgfGw-Rmq__oig58g3t-RsbGizRr0g@mail.gmail.com>

MD (Mean diffusivity) can be obtained by Trace/3.
Or, you can average three eigenvalues (eigenvalue0+eigenvalue1+eigenvalue2)/3.
Obviously, Trace is the sum of these three eigenvalues.

In early days of diffusion-weighted imaging, there were confusions
about apparent diffusion constant, average diffusion constant, and
mean diffusivity. Trace is a technical term that can't be confused.
So, back then, Trace was used often.

On Wed, May 30, 2012 at 5:14 AM, ycq0565 <ycq0565 at 126.com> wrote:
> hi everybody,
> I am a new DTIstudio user,and I need to get the MD map from DTIstudio,if
> anyone can help?
> thanks a lot,and best wishes.
> Dr.Ye--
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>

From santoshyadav20076 at gmail.com  Fri Jun  1 02:49:29 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Fri, 01 Jun 2012 12:19:29 +0530
Subject: [Mristudio-users] Is LDDMM server is available?
Message-ID: <CA+7fnM1c8BU5SB0s68AGW=JDZsiS6Muf6gQVaQJmtJWwNuiJRw@mail.gmail.com>

Hello dti experts,

I am using MRIstudio.

I have uploaded our data to LDDMM server yesterday.

I would like to know the status of LDDMM server. Is it available now?


Regards

santosh

-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From hechmi.abdelmomen at gmail.com  Fri Jun  1 06:26:47 2012
From: hechmi.abdelmomen at gmail.com (hechmi abdelmoumen)
Date: Fri, 01 Jun 2012 11:26:47 +0100
Subject: [Mristudio-users] Is LDDMM server is available?
In-Reply-To: <CA+7fnM1c8BU5SB0s68AGW=JDZsiS6Muf6gQVaQJmtJWwNuiJRw@mail.gmail.com>
References: <CA+7fnM1c8BU5SB0s68AGW=JDZsiS6Muf6gQVaQJmtJWwNuiJRw@mail.gmail.com>
Message-ID: <CA+cfAZyAdBaDiCxJoR448PdyNTbFP4La-1EWUrmC_GD1nJhxrg@mail.gmail.com>

Hello Santosh,

I'm not an MRIstudio expert, I've just learned how to use this soft.
Sorry I can't help you.

Best regards.

2012/6/1 Santosh Yadav <santoshyadav20076 at gmail.com>

> Hello dti experts,
>
> I am using MRIstudio.
>
> I have uploaded our data to LDDMM server yesterday.
>
> I would like to know the status of LDDMM server. Is it available now?
>
>
> Regards
>
> santosh
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>


-- 
Cordialement,
Hechmi Abdelmoumen.
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From xli16 at jhmi.edu  Fri Jun  1 09:23:25 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 01 Jun 2012 09:23:25 -0400
Subject: [Mristudio-users] Is LDDMM server is available?
In-Reply-To: <CA+7fnM1c8BU5SB0s68AGW=JDZsiS6Muf6gQVaQJmtJWwNuiJRw@mail.gmail.com>
References: <CA+7fnM1c8BU5SB0s68AGW=JDZsiS6Muf6gQVaQJmtJWwNuiJRw@mail.gmail.com>
Message-ID: <7270a6ee1daa1.4fc88a0d@johnshopkins.edu>

I just sent a lddmm job to the server. It seems fine. 

Xin

----- Original Message -----
From: Santosh Yadav <santoshyadav20076 at gmail.com>
Date: Friday, June 1, 2012 2:49 am
Subject: [Mristudio-users] Is LDDMM server is available?
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hello dti experts,
>  
>  I am using MRIstudio.
>  
>  I have uploaded our data to LDDMM server yesterday.
>  
>  I would like to know the status of LDDMM server. Is it available now?
>  
>  
>  Regards
>  
>  santosh
>  
>  -- 
>  With Best Regards,
>  
>  Neuroscience and MR Research Program
>  
>  Department of Medicine, Queen's Medical Center
>  
>  University of Hawaii
>  
>  1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>  
>  Phone No. 808-220-7152
>  
>  Fax No.  808-545-8970 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From akolasny at jhu.edu  Fri Jun  1 11:01:10 2012
From: akolasny at jhu.edu (akolasny at jhu.edu)
Date: Fri, 01 Jun 2012 11:01:10 -0400
Subject: [Mristudio-users] Is LDDMM server is available?
In-Reply-To: <7230889719374.4fc89c4d@johnshopkins.edu>
References: <7230889719374.4fc89c4d@johnshopkins.edu>
Message-ID: <148fe75fc371b4d7382b894b754f6ee2.squirrel@webmail.cis.jhu.edu>

The server is functioning. Normally, an email should be sent
in a couple of minutes that processing has started.

Verify that your email address has been registered at the
mristudio.org site. If it is not a valid email address, the
submission is ignored.

If you have the md5sum of the submission, I can check the logs
to verify the submission.

-Anthony


> Hello dti experts,
>
> I am using MRIstudio.
>
> I have uploaded our data to LDDMM server yesterday.
>
> I would like to know the status of LDDMM server. Is it available now?
>
>
> Regards
>
> santosh
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>



From zhaolianxin1985 at 163.com  Fri Jun  1 22:49:32 2012
From: zhaolianxin1985 at 163.com (=?GBK?B?1dTBrNDC?=)
Date: Sat, 02 Jun 2012 10:49:32 +0800 (CST)
Subject: [Mristudio-users] Is LDDMM server is available?
In-Reply-To: <148fe75fc371b4d7382b894b754f6ee2.squirrel@webmail.cis.jhu.edu>
References: <7230889719374.4fc89c4d@johnshopkins.edu>
	<148fe75fc371b4d7382b894b754f6ee2.squirrel@webmail.cis.jhu.edu>
Message-ID: <feb911a.14ce4.137ab190566.Coremail.zhaolianxin1985@163.com>


It seems fine.




At 2012-06-01 23:01:10,akolasny at jhu.edu wrote:
>The server is functioning. Normally, an email should be sent
>in a couple of minutes that processing has started.
>
>Verify that your email address has been registered at the
>mristudio.org site. If it is not a valid email address, the
>submission is ignored.
>
>If you have the md5sum of the submission, I can check the logs
>to verify the submission.
>
>-Anthony
>
>
>> Hello dti experts,
>>
>> I am using MRIstudio.
>>
>> I have uploaded our data to LDDMM server yesterday.
>>
>> I would like to know the status of LDDMM server. Is it available now?
>>
>>
>> Regards
>>
>> santosh
>>
>> --
>> With Best Regards,
>>
>> Neuroscience and MR Research Program
>>
>> Department of Medicine, Queen's Medical Center
>>
>> University of Hawaii
>>
>> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>>
>> Phone No. 808-220-7152
>>
>> Fax No.  808-545-8970
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>
>
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
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From jie.jiang at emory.edu  Tue Jun  5 11:34:05 2012
From: jie.jiang at emory.edu (Jiang, Jie)
Date: Tue, 05 Jun 2012 15:34:05 +0000
Subject: [Mristudio-users] Is LDDMM server is available?
In-Reply-To: <feb911a.14ce4.137ab190566.Coremail.zhaolianxin1985@163.com>
References: <7230889719374.4fc89c4d@johnshopkins.edu>
	<148fe75fc371b4d7382b894b754f6ee2.squirrel@webmail.cis.jhu.edu>
	<feb911a.14ce4.137ab190566.Coremail.zhaolianxin1985@163.com>
Message-ID: <EE3B3A5800B7A946926FDDC1DBAD5C2A23EA54CF@e14mbx12n.Enterprise.emory.net>

Dear all,
I am using DTI studio and have a question about drawing ROI. I selected "ROI Drawing", but no matter what kind of shape I selected, when I put the mouse on the image, it will start to draw, without any click on the mouse. Can anyone please tell me how to avoid this? I only want to draw the area I am interested. Thanks.
Jie
________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of ??? [zhaolianxin1985 at 163.com]
Sent: Friday, June 01, 2012 10:49 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Is LDDMM server is available?


It seems fine.


At 2012-06-01 23:01:10,akolasny at jhu.edu wrote:
>The server is functioning. Normally, an email should be sent
>in a couple of minutes that processing has started.
>
>Verify that your email address has been registered at the
>mristudio.org site. If it is not a valid email address, the
>submission is ignored.
>
>If you have the md5sum of the submission, I can check the logs
>to verify the submission.
>
>-Anthony
>
>
>> Hello dti experts,
>>
>> I am using MRIstudio.
>>
>> I have uploaded our data to LDDMM server yesterday.
>>
>> I would like to know the status of LDDMM server. Is it available now?
>>
>>
>> Regards
>>
>> santosh
>>
>> --
>> With Best Regards,
>>
>> Neuroscience and MR Research Program
>>
>> Department of Medicine, Queen's Medical Center
>>
>> University of Hawaii
>>
>> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>>
>> Phone No. 808-220-7152
>>
>> Fax No.  808-545-8970
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>
>
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org




________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
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If you have received this message in error, please contact
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From fatemeh.derakhshan at gmail.com  Tue Jun  5 18:52:52 2012
From: fatemeh.derakhshan at gmail.com (Fatemeh Derakhshan)
Date: Tue, 05 Jun 2012 17:52:52 -0500
Subject: [Mristudio-users] orientation and direction!
Message-ID: <CAJhfb4zoUyk5himTPb+gCTtEebohf4aAhUYyVgb1soSnReYjWg@mail.gmail.com>

Hi DTI experts
This might be a basic question; but I wonder how orientation and direction
are different in DTI. My protocol says that we uses "30 different
directions" to acquire DTI gradients along "six different orientations" and
then we have three colors to code the directions of diffusion. Can anyone
kindly explain it please!
Thanks

-- 
Fatemeh Derakhshan
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From susumu at mri.jhu.edu  Thu Jun  7 08:40:20 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 07 Jun 2012 08:40:20 -0400
Subject: [Mristudio-users] orientation and direction!
In-Reply-To: <CAJhfb4zoUyk5himTPb+gCTtEebohf4aAhUYyVgb1soSnReYjWg@mail.gmail.com>
References: <CAJhfb4zoUyk5himTPb+gCTtEebohf4aAhUYyVgb1soSnReYjWg@mail.gmail.com>
Message-ID: <CAEq9ap+4ij-pmm47m72A+1EKzXv4AKj5XyaMXi8Zp4jz-AwzyQ@mail.gmail.com>

What you wrote doesn't make sense to me.
"direction" and "orientation" are the same thing. So, if your protocol uses
"30 different directions", that is "30 different orientations", not "six
different orientations". To do DTI you need at least 6 directions
(orientations).

>From these measurements, a vector (fiber orientation) can be measured for
each pixel. The unit vector has x, y, z components, which is visualized by
the three principal colors.

On Tue, Jun 5, 2012 at 6:52 PM, Fatemeh Derakhshan <
fatemeh.derakhshan at gmail.com> wrote:

> Hi DTI experts
> This might be a basic question; but I wonder how orientation and direction
> are different in DTI. My protocol says that we uses "30 different
> directions" to acquire DTI gradients along "six different orientations" and
> then we have three colors to code the directions of diffusion. Can anyone
> kindly explain it please!
> Thanks
>
> --
> Fatemeh Derakhshan
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From gnirkem at upstate.edu  Fri Jun 15 11:00:29 2012
From: gnirkem at upstate.edu (Matthew Gnirke)
Date: Fri, 15 Jun 2012 11:00:29 -0400
Subject: [Mristudio-users] Zooming More
Message-ID: <4FDB15CD0200003D0005AE10@gatedom1.upstate.edu>

Hello,


I have a quick question regarding the zoom feature. Is there any way to make DTI studio allow me to zoom in more? My image dimensions are 128x128 with a FOV of 256x256 and 2x2x2 voxels. When I zoom in to the max amount allowed by DTIstudio (2 clicks of the + icon), the image is still relatively small for ROI drawing. Can I play with the image parameters or anything else to increase the amount that I can zoom, or am I stuck with this view?


Thanks alot!
Matt



From susumu at mri.jhu.edu  Fri Jun 15 13:24:44 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 15 Jun 2012 13:24:44 -0400
Subject: [Mristudio-users] Zooming More
In-Reply-To: <4FDB15CD0200003D0005AE10@gatedom1.upstate.edu>
References: <4FDB15CD0200003D0005AE10@gatedom1.upstate.edu>
Message-ID: <CAEq9apKLKr1EKuovsog6vFDvv8sWJRuP4gTZ7ahjUmQB3xv6vw@mail.gmail.com>

I think the best way is to turn on interpolation (depending on
manufacturers, they call it differently, but technically called
"zerofilling" or "zeropadding", which make the matrix size twice as large)
would be the best way, although you can't do it after scans are done.

For existing data, it is possible to interpolate the data to 256x256 using
a function in DiffeoMap.
Another thing we often recommend is to register all the images to our 1x1x1
mm atlas space so that all your data will have the same brain angles and
locations. This will not only adjust the brain image matrix to 1x1x1
(181x217x181), your manual ROI drawing could be more consistent.

On Fri, Jun 15, 2012 at 11:00 AM, Matthew Gnirke <gnirkem at upstate.edu>wrote:

> Hello,
>
>
> I have a quick question regarding the zoom feature. Is there any way to
> make DTI studio allow me to zoom in more? My image dimensions are 128x128
> with a FOV of 256x256 and 2x2x2 voxels. When I zoom in to the max amount
> allowed by DTIstudio (2 clicks of the + icon), the image is still
> relatively small for ROI drawing. Can I play with the image parameters or
> anything else to increase the amount that I can zoom, or am I stuck with
> this view?
>
>
> Thanks alot!
> Matt
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From dereksohn at gmail.com  Sun Jun 17 03:50:22 2012
From: dereksohn at gmail.com (jeongpyo son)
Date: Sun, 17 Jun 2012 16:50:22 +0900
Subject: [Mristudio-users] About calculating tensors
Message-ID: <57E91997-7292-4748-A390-E8D0D52C5ED8@gmail.com>

Hi. DTI Experts! 
I'm the new researcher at this part.
I have two questions about tensor calculation.

1. 
After acquired the DWIs, I have calculated tensors using the DTI studio program.
But there are problems about calculated data.
At many voxels (about 3/5 of whole FOV), FA values are overestimated. 
FA > 0.7 of gray matter regions and FA = 1 at almost WM regions.
Eigenvalues of overestimated regions are nagative values.
My data was acquired using Bruker 7T MRI and the subject were SD rats.
Why this problems are occurs?
Is the DTI studio program only for human DTI data analysis?

2. 
For solve these problems, I have a plan to calculate the diffusion tensors manually.
I only know the raw DWI data's signal intensities.
Through them, can I calculate the eigenvalues manually? 
If can, please let me know the calculating procedures (with formula). 

I know that my questions are so bottomless pit. 
But I spent many times for solving this problems and hit the wall.
I need your help!!


Thanks a lot!!



From joeh at cis.jhu.edu  Thu Jun 21 16:22:28 2012
From: joeh at cis.jhu.edu (joeh at cis.jhu.edu)
Date: Thu, 21 Jun 2012 16:22:28 -0400
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) Software
	Beta 49 Announcement
In-Reply-To: <35562.173.69.187.127.1328228283.squirrel@webmail.cis.jhu.edu>
References: <35562.173.69.187.127.1328228283.squirrel@webmail.cis.jhu.edu>
Message-ID: <9eb8ffbf0ed50b9c31cfde43f97cb724.squirrel@webmail.cis.jhu.edu>

Computational Anatomy Works (CAWorks) Software Beta 49 Announcement

CAWorks beta 49 is now available for windows 32 and 64 bit, mac osx, and
linux 32 and 64 bit

The new version includes

Addition of tab to dock panel for remote auto-segmentation

Addition of tab to dock panel for remote lddmm-cardiac

Addition of tab to dock panel for remote template-estimation


CAWorks is available through mristudio.org under:

   https://www.mristudio.org/download/binaries/caworks/

The software application Computational Anatomy Works (CAWorks) was
developed to support Computational Anatomy and shape analysis. The
capabilities of CAWorks include:

   1. Interactive landmark placement to create segmentation (mask) of
desired region of interest

   2. Specialized landmark placement plugins for subcortical structures
such as hippocampus and amygdala

   3. Support for multiple Medical Imaging data formats, such as Nifti,
Analyze, Freesurfer, DICOM and landmark data

   4. Quadra Planar view visualization

   5. Shape Analysis plugin modules, such as Large Deformation
Diffeomorphic Metric Mapping (LDDMM)

Current enhancements to CAWorks have focused on interactive support for
landmarking of subcortical structures. Specific plugins are available for
landmark placement of the hippocampus, amygdala and entorhinal cortex
regions. After landmarking is completed, CAWorks facilitates submission
for automated segmentation processing. CAWorks is being used by the
Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
Localization and Biomedical Informatics Research Network (BIRN) projects.

CAWorks extends ParaView, an open source, multi-platform, freely available
program for parallel, interactive, scientific visualization. An important
visualization tool for TeraGrid researchers, its client-server
architecture facilitates remote visualization of datasets and the
generation of level of detail (LOD) models that maintain interactive frame
rates for large datasets.

Tutorials describing CAWorks for the ROI feature are located at:

    http://caportal.cis.jhu.edu/tutorials


If you have questions regarding this software, please put CAWorks in your
subject line for the mristudio-users mailing list.

Thanks!
CAWorks Development Team


From jie.jiang at emory.edu  Thu Jun 21 17:55:50 2012
From: jie.jiang at emory.edu (Jiang, Jie)
Date: Thu, 21 Jun 2012 21:55:50 +0000
Subject: [Mristudio-users] FA map problem
Message-ID: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>

Dear all,
I am using DTIStudio to get the FA image. The primary images are ok. However, after calculating, the FA maps are always much blur with pretty low resolution. Does anyone know how to improve the resolution or any suggestion? Thanks a lot.
Best,
Jie

________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
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From susumu at mri.jhu.edu  Thu Jun 21 18:17:37 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 21 Jun 2012 18:17:37 -0400
Subject: [Mristudio-users] FA map problem
In-Reply-To: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
Message-ID: <CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>

I recommend to do 2x interpolation (time-domain, not image-domain
interpolation, also called zerofilling or zeropadding) at the data
acquisition.  Unfortunately, you have to do this in the scanner.

On Thu, Jun 21, 2012 at 5:55 PM, Jiang, Jie <jie.jiang at emory.edu> wrote:

>  Dear all,
> I am using DTIStudio to get the FA image. The primary images are ok.
> However, after calculating, the FA maps are always much blur with pretty
> low resolution. Does anyone know how to improve the resolution or any
> suggestion? Thanks a lot.
> Best,
> Jie
>
> ------------------------------
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From jie.jiang at emory.edu  Fri Jun 22 09:29:24 2012
From: jie.jiang at emory.edu (Jiang, Jie)
Date: Fri, 22 Jun 2012 13:29:24 +0000
Subject: [Mristudio-users] FA map problem
In-Reply-To: <CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
	<CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
Message-ID: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E4550@e14mbx10n.Enterprise.emory.net>

Thanks for the response. So you mean I have to do this when I was doing the scan and  there is no way to optimize the images during the processing?Thanks
________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of susumu mori [susumu at mri.jhu.edu]
Sent: Thursday, June 21, 2012 6:17 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] FA map problem

I recommend to do 2x interpolation (time-domain, not image-domain interpolation, also called zerofilling or zeropadding) at the data acquisition.  Unfortunately, you have to do this in the scanner.

On Thu, Jun 21, 2012 at 5:55 PM, Jiang, Jie <jie.jiang at emory.edu<mailto:jie.jiang at emory.edu>> wrote:
Dear all,
I am using DTIStudio to get the FA image. The primary images are ok. However, after calculating, the FA maps are always much blur with pretty low resolution. Does anyone know how to improve the resolution or any suggestion? Thanks a lot.
Best,
Jie

________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>


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From susumu at mri.jhu.edu  Fri Jun 22 10:56:52 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 22 Jun 2012 10:56:52 -0400
Subject: [Mristudio-users] FA map problem
In-Reply-To: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E4550@e14mbx10n.Enterprise.emory.net>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
	<CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
	<EE3B3A5800B7A946926FDDC1DBAD5C2A380E4550@e14mbx10n.Enterprise.emory.net>
Message-ID: <CAEq9ap+TPVbY1zqDs4bw6rSxnr12zkm=i_qsiE1nKRFAfSP34w@mail.gmail.com>

well, you can always do image-domain interpolation. I'm not sure if it
looks as pretty as the time-domain interpolation by scanners. Some people
say that they are the same thing.

One thing I can comment is, if you will use our atlas-based pipeline for
image quantification, regardless of your image resolution, they are all
resampled to 1x1x1 mm / 181x217x181, as defined by the MNI coordinates. So,
you can just proceed to our MriStudio pipeline without any interpolation.
You feed in your 2.5 mm resolution data and 1mm data will come out.

On Fri, Jun 22, 2012 at 9:29 AM, Jiang, Jie <jie.jiang at emory.edu> wrote:

>  Thanks for the response. So you mean I have to do this when I was doing
> the scan and  there is no way to optimize the images during the
> processing?Thanks
>  ------------------------------
> *From:* mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] on behalf of susumu mori [
> susumu at mri.jhu.edu]
> *Sent:* Thursday, June 21, 2012 6:17 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] FA map problem
>
>  I recommend to do 2x interpolation (time-domain, not image-domain
> interpolation, also called zerofilling or zeropadding) at the data
> acquisition.  Unfortunately, you have to do this in the scanner.
>
> On Thu, Jun 21, 2012 at 5:55 PM, Jiang, Jie <jie.jiang at emory.edu> wrote:
>
>>  Dear all,
>> I am using DTIStudio to get the FA image. The primary images are ok.
>> However, after calculating, the FA maps are always much blur with pretty
>> low resolution. Does anyone know how to improve the resolution or any
>> suggestion? Thanks a lot.
>> Best,
>> Jie
>>
>> ------------------------------
>>
>> This e-mail message (including any attachments) is for the sole use of
>> the intended recipient(s) and may contain confidential and privileged
>> information. If the reader of this message is not the intended
>> recipient, you are hereby notified that any dissemination, distribution
>> or copying of this message (including any attachments) is strictly
>> prohibited.
>>
>> If you have received this message in error, please contact
>> the sender by reply e-mail message and destroy all copies of the
>> original message (including attachments).
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From raviteja.kotikalapudi at gmail.com  Fri Jun 22 11:10:39 2012
From: raviteja.kotikalapudi at gmail.com (Kotikalapudi Raviteja)
Date: Fri, 22 Jun 2012 16:10:39 +0100
Subject: [Mristudio-users] FA map problem
In-Reply-To: <CAEq9ap+TPVbY1zqDs4bw6rSxnr12zkm=i_qsiE1nKRFAfSP34w@mail.gmail.com>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
	<CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
	<EE3B3A5800B7A946926FDDC1DBAD5C2A380E4550@e14mbx10n.Enterprise.emory.net>
	<CAEq9ap+TPVbY1zqDs4bw6rSxnr12zkm=i_qsiE1nKRFAfSP34w@mail.gmail.com>
Message-ID: <CAGJ50wYdKWB=GAwZo01SaGK9ZhiKOsiXJd_CVcKZpz1uUFdfQw@mail.gmail.com>

Dear Susumu,

I am a new student to the field of MR imaging. As of now, I am doing a
research where I have used SPM and DTI Studio to coregister and normalize
the images. I used the JHU parcellation in MRI Cro to extract the various
regions of interest. Now I have certain parameters such as ROI n, mean and
ROI SD. Could you please let me know a way to calculate FA, ADC values so
that I could draw various conclusions and comparisons.

Regards,
Ravi

On Fri, Jun 22, 2012 at 3:56 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> well, you can always do image-domain interpolation. I'm not sure if it
> looks as pretty as the time-domain interpolation by scanners. Some people
> say that they are the same thing.
>
> One thing I can comment is, if you will use our atlas-based pipeline for
> image quantification, regardless of your image resolution, they are all
> resampled to 1x1x1 mm / 181x217x181, as defined by the MNI coordinates. So,
> you can just proceed to our MriStudio pipeline without any interpolation.
> You feed in your 2.5 mm resolution data and 1mm data will come out.
>
>
> On Fri, Jun 22, 2012 at 9:29 AM, Jiang, Jie <jie.jiang at emory.edu> wrote:
>
>>  Thanks for the response. So you mean I have to do this when I was doing
>> the scan and  there is no way to optimize the images during the
>> processing?Thanks
>>  ------------------------------
>> *From:* mristudio-users-bounces at mristudio.org [
>> mristudio-users-bounces at mristudio.org] on behalf of susumu mori [
>> susumu at mri.jhu.edu]
>> *Sent:* Thursday, June 21, 2012 6:17 PM
>> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> *Subject:* Re: [Mristudio-users] FA map problem
>>
>>  I recommend to do 2x interpolation (time-domain, not image-domain
>> interpolation, also called zerofilling or zeropadding) at the data
>> acquisition.  Unfortunately, you have to do this in the scanner.
>>
>> On Thu, Jun 21, 2012 at 5:55 PM, Jiang, Jie <jie.jiang at emory.edu> wrote:
>>
>>>  Dear all,
>>> I am using DTIStudio to get the FA image. The primary images are ok.
>>> However, after calculating, the FA maps are always much blur with pretty
>>> low resolution. Does anyone know how to improve the resolution or any
>>> suggestion? Thanks a lot.
>>> Best,
>>> Jie
>>>
>>> ------------------------------
>>>
>>> This e-mail message (including any attachments) is for the sole use of
>>> the intended recipient(s) and may contain confidential and privileged
>>> information. If the reader of this message is not the intended
>>> recipient, you are hereby notified that any dissemination, distribution
>>> or copying of this message (including any attachments) is strictly
>>> prohibited.
>>>
>>> If you have received this message in error, please contact
>>> the sender by reply e-mail message and destroy all copies of the
>>> original message (including attachments).
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From santoshyadav20076 at gmail.com  Sun Jun 24 04:24:11 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Sun, 24 Jun 2012 13:54:11 +0530
Subject: [Mristudio-users] Tensor calculation
Message-ID: <CA+7fnM3P1VLSx=u7Li1sHK7FOhpfqeQu=8A9kkXmconKhm7kzQ@mail.gmail.com>

Hello DTI Experts,

I want to know which method is good for tensor calculation using DTI-Studio
for LDDMM.

In DTI-Studio, for tensor calculation there are four methods:

1. Standard linear registration
2. Automatic outlier SLIC rejection
3. Automatic outlier pixel rejection method
4. AIR for theory-original DWI pair with using a 12-mode affine
transformation (Woods et al., 1998)

I read few articles which described the tensor calculation by using AIR for
theory-original DWI pair Method (Method 4) (Neuroimage 2009; 47(2):
618-627, Neuroimage 2009; 46(2): 486-499), is this method having any
advantage over Automatic outlier pixel rejection method?

With Best Regards


-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From santoshyadav20076 at gmail.com  Mon Jun 25 16:18:19 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Mon, 25 Jun 2012 10:18:19 -1000
Subject: [Mristudio-users] Tensor calculation
In-Reply-To: <DD7AC5C501BF624E8FA2BC897D4FA74C0123DE@RAD-EXCH-SRV14.win.ad.jhu.edu>
References: <CA+7fnM3P1VLSx=u7Li1sHK7FOhpfqeQu=8A9kkXmconKhm7kzQ@mail.gmail.com>
	<DD7AC5C501BF624E8FA2BC897D4FA74C0123DE@RAD-EXCH-SRV14.win.ad.jhu.edu>
Message-ID: <CA+7fnM3f1_L5+yxHqvEdoOg9xnzo5xbU0-EiDmJfHKC57cFAhQ@mail.gmail.com>

Dear Dr Hangyi,

Lot of thanks for great response.

I have another question regarding DTI processing.

I am processing the DTI data acquired from Siemens 3T for LDDMM, Is it
necessary/important step to do the Automatic image registration using a
12-mode affine transformation before tensor calculation?

As I read the articles, It is important step for motion and eddy current
distortion correction in the DTI data.

Ref.
1. Neuroimage 2009; 47(2): 618-627
2. Jiang H<http://www.ncbi.nlm.nih.gov/pubmed?term=Jiang%20H%5BAuthor%5D&cauthor=true&cauthor_uid=16413083>Comput
Methods Programs Biomed. 2006, 81(2):106-16


With Best Regards

Santosh



On Mon, Jun 25, 2012 at 4:50 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:

>
> there is no standard answer for your question, it depends on original
> dataset.  the following recommends are just for your reference:
>
> if your dataset has only few diffusion orientations (e.g. less than 8),
> you may try:
> manual image quality check + standard linear fitting or outlier pixel
> rejection method;
>
> if you have only few subjects to study, you way try:
> manual image quality check + standard linear fitting;
>
> if your dataset have a lot of DW orientations (e.g. more than 15), you can
> try:
> outlier slice rejection method;
>
> if you find motion artifact, you can  use AIR based method.
>
> and......
>
> best,
>
>
> hangyi
>
>
>
>
>
>
>  or outlier pixel rejection method;
>
>
> ________________________________
> From: mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] on behalf of Santosh Yadav [
> santoshyadav20076 at gmail.com]
> Sent: Sunday, June 24, 2012 4:24 AM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: [Mristudio-users] Tensor calculation
>
> Hello DTI Experts,
>
> I want to know which method is good for tensor calculation using
> DTI-Studio for LDDMM.
>
> In DTI-Studio, for tensor calculation there are four methods:
>
> 1. Standard linear registration
> 2. Automatic outlier SLIC rejection
> 3. Automatic outlier pixel rejection method
> 4. AIR for theory-original DWI pair with using a 12-mode affine
> transformation (Woods et al., 1998)
>
> I read few articles which described the tensor calculation by using AIR
> for theory-original DWI pair Method (Method 4) (Neuroimage 2009; 47(2):
> 618-627, Neuroimage 2009; 46(2): 486-499), is this method having any
> advantage over Automatic outlier pixel rejection method?
>
> With Best Regards
>
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
>
>
>
>


-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From tangyan at csu.edu.cn  Mon Jul  2 21:15:03 2012
From: tangyan at csu.edu.cn (=?GBK?B?zMbR3g==?=)
Date: Tue, 03 Jul 2012 09:15:03 +0800 (CST)
Subject: [Mristudio-users] help me for MRIconvert
Message-ID: <10244746.1571781341278103827.JavaMail.coremail@app2>

hello expert!

I got several dti-datasets (12 directions) by Siemens avanto and want to get the  gradient table.   
The data were obtained by mosaic. So extract bvecs with micron and MRIconvert. But I find the results are different.
Would you help me ?
And I track the fiber in   Diffusion Toolkit ,but no resluts.
if the data were obtained by no mosaic, How can i extract bvecs ?
thank for you help


From susumu at mri.jhu.edu  Wed Jul  4 15:18:24 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 04 Jul 2012 15:18:24 -0400
Subject: [Mristudio-users] Tensor calculation
In-Reply-To: <CA+7fnM3f1_L5+yxHqvEdoOg9xnzo5xbU0-EiDmJfHKC57cFAhQ@mail.gmail.com>
References: <CA+7fnM3P1VLSx=u7Li1sHK7FOhpfqeQu=8A9kkXmconKhm7kzQ@mail.gmail.com>
	<DD7AC5C501BF624E8FA2BC897D4FA74C0123DE@RAD-EXCH-SRV14.win.ad.jhu.edu>
	<CA+7fnM3f1_L5+yxHqvEdoOg9xnzo5xbU0-EiDmJfHKC57cFAhQ@mail.gmail.com>
Message-ID: <CAEq9apJG_F_WbcHYTu2++xj7e=kt9Jg_ipBvSYxWytsPjhm6sA@mail.gmail.com>

It is a common practice to perform 12-mode affine before tensor
calculation. If your scanner doesn't have noticeable eddy current (like
many modern Siemens), you can do 6-mode rigid just for motion correction.

On Mon, Jun 25, 2012 at 4:18 PM, Santosh Yadav
<santoshyadav20076 at gmail.com>wrote:

> Dear Dr Hangyi,
>
> Lot of thanks for great response.
>
> I have another question regarding DTI processing.
>
> I am processing the DTI data acquired from Siemens 3T for LDDMM, Is it
> necessary/important step to do the Automatic image registration using a
> 12-mode affine transformation before tensor calculation?
>
> As I read the articles, It is important step for motion and eddy current
> distortion correction in the DTI data.
>
> Ref.
> 1. Neuroimage 2009; 47(2): 618-627
> 2. Jiang H<http://www.ncbi.nlm.nih.gov/pubmed?term=Jiang%20H%5BAuthor%5D&cauthor=true&cauthor_uid=16413083>Comput Methods Programs Biomed. 2006, 81(2):106-16
>
>
> With Best Regards
>
> Santosh
>
>
>
> On Mon, Jun 25, 2012 at 4:50 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:
>
>>
>> there is no standard answer for your question, it depends on original
>> dataset.  the following recommends are just for your reference:
>>
>> if your dataset has only few diffusion orientations (e.g. less than 8),
>> you may try:
>> manual image quality check + standard linear fitting or outlier pixel
>> rejection method;
>>
>> if you have only few subjects to study, you way try:
>> manual image quality check + standard linear fitting;
>>
>> if your dataset have a lot of DW orientations (e.g. more than 15), you
>> can try:
>> outlier slice rejection method;
>>
>> if you find motion artifact, you can  use AIR based method.
>>
>> and......
>>
>> best,
>>
>>
>> hangyi
>>
>>
>>
>>
>>
>>
>>  or outlier pixel rejection method;
>>
>>
>> ________________________________
>> From: mristudio-users-bounces at mristudio.org [
>> mristudio-users-bounces at mristudio.org] on behalf of Santosh Yadav [
>> santoshyadav20076 at gmail.com]
>> Sent: Sunday, June 24, 2012 4:24 AM
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: [Mristudio-users] Tensor calculation
>>
>>
>> Hello DTI Experts,
>>
>> I want to know which method is good for tensor calculation using
>> DTI-Studio for LDDMM.
>>
>> In DTI-Studio, for tensor calculation there are four methods:
>>
>> 1. Standard linear registration
>> 2. Automatic outlier SLIC rejection
>> 3. Automatic outlier pixel rejection method
>> 4. AIR for theory-original DWI pair with using a 12-mode affine
>> transformation (Woods et al., 1998)
>>
>> I read few articles which described the tensor calculation by using AIR
>> for theory-original DWI pair Method (Method 4) (Neuroimage 2009; 47(2):
>> 618-627, Neuroimage 2009; 46(2): 486-499), is this method having any
>> advantage over Automatic outlier pixel rejection method?
>>
>> With Best Regards
>>
>>
>> --
>> With Best Regards,
>>
>> Neuroscience and MR Research Program
>>
>> Department of Medicine, Queen's Medical Center
>>
>> University of Hawaii
>>
>> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>>
>> Phone No. 808-220-7152
>>
>> Fax No.  808-545-8970
>>
>>
>>
>>
>
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Wed Jul  4 15:25:21 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 04 Jul 2012 15:25:21 -0400
Subject: [Mristudio-users] help me for MRIconvert
In-Reply-To: <10244746.1571781341278103827.JavaMail.coremail@app2>
References: <10244746.1571781341278103827.JavaMail.coremail@app2>
Message-ID: <CAEq9apKKS7kHSNU=44NctCHs-0F1MPnCWCG93mQRASWh46ojTg@mail.gmail.com>

Because there are several tricky problems related to gradient tables, I
suggest you not to combine programs from different sources. If you extract
b-vector information by MRIcro and feed the results into DtiStudio, we
can't guarantee the correctness.

You'd better do all calculation within one program platform. If you want to
use DtiStudio, it can read Siemens Mosaic, extract b-table, check b-table
recalculation option if you are using oblique imaging, and you are ready
for tensor calculation.

On Mon, Jul 2, 2012 at 9:15 PM, ?? <tangyan at csu.edu.cn> wrote:

> hello expert!
>
> I got several dti-datasets (12 directions) by Siemens avanto and want to
> get the  gradient table.
> The data were obtained by mosaic. So extract bvecs with micron and
> MRIconvert. But I find the results are different.
> Would you help me ?
> And I track the fiber in   Diffusion Toolkit ,but no resluts.
> if the data were obtained by no mosaic, How can i extract bvecs ?
> thank for you help
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From raviteja.kotikalapudi at gmail.com  Tue Jul 10 13:16:35 2012
From: raviteja.kotikalapudi at gmail.com (Kotikalapudi Raviteja)
Date: Tue, 10 Jul 2012 18:16:35 +0100
Subject: [Mristudio-users] help me for MRIconvert
In-Reply-To: <CAEq9apKKS7kHSNU=44NctCHs-0F1MPnCWCG93mQRASWh46ojTg@mail.gmail.com>
References: <10244746.1571781341278103827.JavaMail.coremail@app2>
	<CAEq9apKKS7kHSNU=44NctCHs-0F1MPnCWCG93mQRASWh46ojTg@mail.gmail.com>
Message-ID: <CAGJ50waokO8ymghiB8NmUT3i5Cuwk5Ct9SggtiQiw3C-uqAX2Q@mail.gmail.com>

Dear Susumu,

I would like to know what kind of software do you suggest me for neonatal
brain image registration.

Thnak you
---ravi

On Wed, Jul 4, 2012 at 8:25 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Because there are several tricky problems related to gradient tables, I
> suggest you not to combine programs from different sources. If you extract
> b-vector information by MRIcro and feed the results into DtiStudio, we
> can't guarantee the correctness.
>
> You'd better do all calculation within one program platform. If you want
> to use DtiStudio, it can read Siemens Mosaic, extract b-table, check
> b-table recalculation option if you are using oblique imaging, and you are
> ready for tensor calculation.
>
> On Mon, Jul 2, 2012 at 9:15 PM, ?? <tangyan at csu.edu.cn> wrote:
>
>> hello expert!
>>
>> I got several dti-datasets (12 directions) by Siemens avanto and want to
>> get the  gradient table.
>> The data were obtained by mosaic. So extract bvecs with micron and
>> MRIconvert. But I find the results are different.
>> Would you help me ?
>> And I track the fiber in   Diffusion Toolkit ,but no resluts.
>> if the data were obtained by no mosaic, How can i extract bvecs ?
>> thank for you help
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Tue Jul 10 16:28:06 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 10 Jul 2012 16:28:06 -0400
Subject: [Mristudio-users] help me for MRIconvert
In-Reply-To: <CAGJ50waokO8ymghiB8NmUT3i5Cuwk5Ct9SggtiQiw3C-uqAX2Q@mail.gmail.com>
References: <10244746.1571781341278103827.JavaMail.coremail@app2>
	<CAEq9apKKS7kHSNU=44NctCHs-0F1MPnCWCG93mQRASWh46ojTg@mail.gmail.com>
	<CAGJ50waokO8ymghiB8NmUT3i5Cuwk5Ct9SggtiQiw3C-uqAX2Q@mail.gmail.com>
Message-ID: <CAEq9apKUh9ST78CRtsHk+OhNr4_NeBXTwFg1QssWn-_S2VARKA@mail.gmail.com>

well, my answer is biased because I think you should use our registration
program, MriStudio.


On Tue, Jul 10, 2012 at 1:16 PM, Kotikalapudi Raviteja <
raviteja.kotikalapudi at gmail.com> wrote:

> Dear Susumu,
>
> I would like to know what kind of software do you suggest me for neonatal
> brain image registration.
>
> Thnak you
> ---ravi
>
> On Wed, Jul 4, 2012 at 8:25 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Because there are several tricky problems related to gradient tables, I
>> suggest you not to combine programs from different sources. If you extract
>> b-vector information by MRIcro and feed the results into DtiStudio, we
>> can't guarantee the correctness.
>>
>> You'd better do all calculation within one program platform. If you want
>> to use DtiStudio, it can read Siemens Mosaic, extract b-table, check
>> b-table recalculation option if you are using oblique imaging, and you are
>> ready for tensor calculation.
>>
>> On Mon, Jul 2, 2012 at 9:15 PM, ?? <tangyan at csu.edu.cn> wrote:
>>
>>> hello expert!
>>>
>>> I got several dti-datasets (12 directions) by Siemens avanto and want to
>>> get the  gradient table.
>>> The data were obtained by mosaic. So extract bvecs with micron and
>>> MRIconvert. But I find the results are different.
>>> Would you help me ?
>>> And I track the fiber in   Diffusion Toolkit ,but no resluts.
>>> if the data were obtained by no mosaic, How can i extract bvecs ?
>>> thank for you help
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
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>
>
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From dereksohn at gmail.com  Sun Jul 15 23:20:44 2012
From: dereksohn at gmail.com (Jeong Pyo Son)
Date: Mon, 16 Jul 2012 12:20:44 +0900
Subject: [Mristudio-users] about Tractography
Message-ID: <CAPyDz4q2Uo5v-KP1vMb4Za0GUs9Qx_uuZTgo2ZkHB9BgXumm8w@mail.gmail.com>

Hello DTI experts!

I'm Jeongpyo Son.

I have some questions regarding* how to acquire tractography data using
homemade calculated images*.
For tensor calculations, DTI studio cannot calculate my DTI data (rat DTI
data acquired by using Bruker 7T scanner) correctly.
Hangyi gave me some advice about calculating tensor using DTI studio but
unfortunately it didn't help. (Regardless of the results, I sincerely
appreciate your help Hangyi ^^)
So, I made MATLAB M-files and acquired the FA, tensor (Dxx, Dyy, Dzz,
.....) and directional diffusivity maps and I saved all the calculated data
in the nii format.

Now, here are some questions that I have about fiber tracking methods:

1. As far as  I know, fiber tracking is available* by tensor images (Dxx,
Dyy, Dzz, .....).*
*How can I create fiber tracts using tensor images?*
My tensor images are 3D so the number of tensor images is 6(Dxx, Dyy, Dzz,
Dxy, Dxz, Dyz).
In the fiber tracking menu, only 1 image can be chosen in the "Tensor
Image" tab.
Should I convert my Tensor images to 4D? If so, then how should I
arrange the Tensor images?

2. Another method, *using principal vector and FA map.*
I made the FA map using my own M-files but I don't know how to create the
principal vector map.
The calculation method of the M-file are same as following.
----------------------------------------------------------------------------------------------------------------------------------------------------
          for z = 1:dz
            for y = 1:dy
              for x = 1:dx
                y_temp = [log(S1(x,y,z)); log(S2(x,y,z)); log(S3(x,y,z));
log(S4(x,y,z)); log(S5(x,y,z)); log(S6(x,y,z))];
                D = inv(b_matrix)*y_temp;
                Dxx(x,y,z) = D(1,1);
                Dyy(x,y,z) = D(2,1);
                Dzz(x,y,z) = D(3,1);
                Dxy(x,y,z) = D(4,1);
                Dxz(x,y,z) = D(5,1);
                Dyz(x,y,z) = D(6,1);
              end
           end
         end
-------------------------------------------------------------------------------------------------------------------------------------------------------
This M-file is made for calculating the data acquired using 6 diffusion
encoding gradients scheme, and S# means "signal of the original DWI/signals
of the b0 image".
So, y_temp means ln(S/S0).

After the Tensor calculations, the eigen values and eigen vectors are
acquired.
*The eigen vectors are formed as 3x3 matrix and by them, how can I acquire
principal eigen vectors?*
Please let me know the formula for calculating principal eigen vector.



Best Wishes.
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From liuyuan0322 at gmail.com  Tue Jul 17 17:12:47 2012
From: liuyuan0322 at gmail.com (yuan liu)
Date: Tue, 17 Jul 2012 16:12:47 -0500
Subject: [Mristudio-users] ROI sequence in the binary map
Message-ID: <CAGbCsyXng2emDPFH-7bH6Gj6CMFTiUzvQ7TqESqsqoW1uJ8J2g@mail.gmail.com>

Hi,

I have a question about the ROI sequence in the binary map loaded in DTI
Studio. Is the first ROI has to be an "OR" ROI? I have five ROIs, one "OR",
three "AND", one "NOT". It seems that if I put "OR" ROI at different place
in the binary map (e.g., be the first one or second one), the fiber results
are different. This is really confusing to me.

Thanks,

Best,
Yuan
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From susumu at mri.jhu.edu  Thu Jul 19 07:54:42 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 19 Jul 2012 07:54:42 -0400
Subject: [Mristudio-users] ROI sequence in the binary map
In-Reply-To: <CAGbCsyXng2emDPFH-7bH6Gj6CMFTiUzvQ7TqESqsqoW1uJ8J2g@mail.gmail.com>
References: <CAGbCsyXng2emDPFH-7bH6Gj6CMFTiUzvQ7TqESqsqoW1uJ8J2g@mail.gmail.com>
Message-ID: <CAEq9ap+9kF=V0Sf73U1X5GmETCCkGqpUBnoGRxyMJ3pPFpYqFA@mail.gmail.com>

Hi Yuan,

Yes, the first one has to be OR. Otherwise, you can't initiate a tracking.
I think your question can be simplified as;

> suppose you have two ROIs, say A and B
> if you set ROI A first, it becomes "OR" and B becomes "AND"
> if you set ROI B first, it becomes "OR" and A becomes "AND"
> question is, whether these two results are different or not.
This is a good question. I assume these should be the same. Have you seen
difference in this kind of simple cases?

On Tue, Jul 17, 2012 at 5:12 PM, yuan liu <liuyuan0322 at gmail.com> wrote:

> Hi,
>
> I have a question about the ROI sequence in the binary map loaded in DTI
> Studio. Is the first ROI has to be an "OR" ROI? I have five ROIs, one "OR",
> three "AND", one "NOT". It seems that if I put "OR" ROI at different place
> in the binary map (e.g., be the first one or second one), the fiber results
> are different. This is really confusing to me.
>
> Thanks,
>
> Best,
> Yuan
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From joeh at cis.jhu.edu  Tue Jul 24 14:22:01 2012
From: joeh at cis.jhu.edu (joeh at cis.jhu.edu)
Date: Tue, 24 Jul 2012 14:22:01 -0400
Subject: [Mristudio-users] Computational Anatomy Works (CAWorks) Software
	Beta 50 Announcement
Message-ID: <b65d659d1e5b07d966849343410e3635.squirrel@webmail.cis.jhu.edu>

Computational Anatomy Works (CAWorks) Software Beta 50 Announcement

CAWorks beta 50 is now available for windows 32 and 64 bit, mac osx, and
linux 32 and 64 bit

The new version includes

Bug fixes for XnatBrowser plugin

Bug fixes for remote template-estimation

Upgrade external libcurl on linux and macosx

Upgrade external openssl support for libcurl on linux and macosx

Change atlas selection in auto-segmentation to single selection list


CAWorks is available through mristudio.org under:

   https://www.mristudio.org/download/binaries/caworks/

The software application Computational Anatomy Works (CAWorks) was
developed to support Computational Anatomy and shape analysis. The
capabilities of CAWorks include:

   1. Interactive landmark placement to create segmentation (mask) of
desired region of interest

   2. Specialized landmark placement plugins for subcortical structures
such as hippocampus and amygdala

   3. Support for multiple Medical Imaging data formats, such as Nifti,
Analyze, Freesurfer, DICOM and landmark data

   4. Quadra Planar view visualization

   5. Shape Analysis plugin modules, such as Large Deformation
Diffeomorphic Metric Mapping (LDDMM)

Current enhancements to CAWorks have focused on interactive support for
landmarking of subcortical structures. Specific plugins are available for
landmark placement of the hippocampus, amygdala and entorhinal cortex
regions. After landmarking is completed, CAWorks facilitates submission
for automated segmentation processing. CAWorks is being used by the
Biomarkers for Older Controls At Risk for Dementia (BIOCARD), Resource for
Quantitative Functional MRI: TRD4, Validation of Structural/Functional MRI
Localization and Biomedical Informatics Research Network (BIRN) projects.

CAWorks extends ParaView, an open source, multi-platform, freely available
program for parallel, interactive, scientific visualization. An important
visualization tool for TeraGrid researchers, its client-server
architecture facilitates remote visualization of datasets and the
generation of level of detail (LOD) models that maintain interactive frame
rates for large datasets.

Tutorials describing CAWorks for the ROI feature are located at:

    http://caportal.cis.jhu.edu/tutorials


If you have questions regarding this software, please put CAWorks in your
subject line for the mristudio-users mailing list.

Thanks!
CAWorks Development Team


From farshidfar at sums.ac.ir  Fri Jul 27 03:25:58 2012
From: farshidfar at sums.ac.ir (farshidfar at sums.ac.ir)
Date: Fri, 27 Jul 2012 11:55:58 +0430
Subject: [Mristudio-users] gradient table
Message-ID: <0c898f4d00344bd364a6b97bc87333bf.squirrel@mail.sums.ac.ir>

Hello all
could you do me a fovour, if someone has gradient table for
Siemense,Aspino,1.5 tesla with 256 independent gradient directions,would
it be possible to send it to me. And do you know that if i used only 64
gradient directions of 256,how can i use this gradient table?
Thank you so much.
regards


-----------------------------------------
This email was sent using SquirrelMail.
   "Webmail for nuts!"
http://squirrelmail.org/

From lili.he2012 at gmail.com  Fri Jul 27 20:49:57 2012
From: lili.he2012 at gmail.com (Lili He)
Date: Fri, 27 Jul 2012 20:49:57 -0400
Subject: [Mristudio-users] kjbb
Message-ID: <5BE535BB-29BB-441F-8CBD-5F79A56A5149@gmail.com>



Sent from my iPhone

From archaeopteryxdin at 163.com  Sat Jul 28 03:54:53 2012
From: archaeopteryxdin at 163.com (archaeopteryxdin at 163.com)
Date: Sat, 28 Jul 2012 15:54:53 +0800
Subject: [Mristudio-users] gradient table
Message-ID: <krj56d7mnj3sqr9r627b6v8q.1343462093707@email.android.com>

you can generate gradient table when you transform raw data by mricron or mriconvert

farshidfar at sums.ac.ir???

>Hello all
>could you do me a fovour, if someone has gradient table for
>Siemense,Aspino,1.5 tesla with 256 independent gradient directions,would
>it be possible to send it to me. And do you know that if i used only 64
>gradient directions of 256,how can i use this gradient table?
>Thank you so much.
>regards
>
>
>-----------------------------------------
>This email was sent using SquirrelMail.
>   "Webmail for nuts!"
>http://squirrelmail.org/
>_______________________________________________
>mristudio-users mailing list
>mristudio-users at mristudio.org
>http://lists.mristudio.org/mailman/listinfo/
>Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org


From ardalanv at gmail.com  Mon Jul 30 06:14:49 2012
From: ardalanv at gmail.com (Ardalan Vossoughi)
Date: Mon, 30 Jul 2012 06:14:49 -0400
Subject: [Mristudio-users] gradient table
In-Reply-To: <0c898f4d00344bd364a6b97bc87333bf.squirrel@mail.sums.ac.ir>
References: <0c898f4d00344bd364a6b97bc87333bf.squirrel@mail.sums.ac.ir>
Message-ID: <CAG=j9q22b5c2__wmvL6viP0GtpOxhbWTqa1yuAatSu9Xkfthew@mail.gmail.com>

Salaam
I am not sure if this necessarily works with Siemens but give it a chance;
good luck doki jun

http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html
Best
AV

On Fri, Jul 27, 2012 at 3:25 AM, <farshidfar at sums.ac.ir> wrote:

> Hello all
> could you do me a fovour, if someone has gradient table for
> Siemense,Aspino,1.5 tesla with 256 independent gradient directions,would
> it be possible to send it to me. And do you know that if i used only 64
> gradient directions of 256,how can i use this gradient table?
> Thank you so much.
> regards
>
>
> -----------------------------------------
> This email was sent using SquirrelMail.
>    "Webmail for nuts!"
> http://squirrelmail.org/
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From jsadino.queens at gmail.com  Mon Jul 30 14:47:10 2012
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Mon, 30 Jul 2012 08:47:10 -1000
Subject: [Mristudio-users] Inverse Linear Transforms
Message-ID: <CAAK1Nke1h=J5KRsSJhjrBgZHXq8HGhFsnaiaqim_xYkgCQ5dNQ@mail.gmail.com>

Hello,

When I apply an inverse linear transform, I would like the Type II ROI map
to go from 181x217x181 to 128x128x28.  What happens is that the ROI part
does get shrunk down, but the image gets zero-padded and remains at
181x217x181.  Is this normal behavior?  Is there any way to shrink the
actual dimensions of the ROI map down to 128x128x28?

Thank You,
Jeff Sadino
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From jsadino.queens at gmail.com  Mon Jul 30 16:42:05 2012
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Mon, 30 Jul 2012 10:42:05 -1000
Subject: [Mristudio-users] MultiChannel LDDMM
Message-ID: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>

Hello,

I am wondering why we only submit the FA and the Trace images.  It seems
like we could submit the FA, Color, DWI, and Trace images.  I see that the
information from these images come from the same "primary channel", but in
my testing, the more images I submit, the better registration I get.  Is
there anything wrong with submitting all four of these channels?

Thank You,
Jeff Sadino
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From jsadino.queens at gmail.com  Mon Jul 30 16:46:47 2012
From: jsadino.queens at gmail.com (Jeff Sadino)
Date: Mon, 30 Jul 2012 10:46:47 -1000
Subject: [Mristudio-users] MultiChannel LDDMM
In-Reply-To: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>
References: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>
Message-ID: <CAAK1NkdxuNFaUx9t2GCJEoi0xUzHw-+775_Y3FsixDcsqN3+ew@mail.gmail.com>

PS: Minus the Color image because that cannot be converted to Byte format.

On Mon, Jul 30, 2012 at 10:42 AM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello,
>
> I am wondering why we only submit the FA and the Trace images.  It seems
> like we could submit the FA, Color, DWI, and Trace images.  I see that the
> information from these images come from the same "primary channel", but in
> my testing, the more images I submit, the better registration I get.  Is
> there anything wrong with submitting all four of these channels?
>
> Thank You,
> Jeff Sadino
>
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From xli16 at jhmi.edu  Mon Jul 30 16:59:34 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Mon, 30 Jul 2012 16:59:34 -0400
Subject: [Mristudio-users] Inverse Linear Transforms
In-Reply-To: <CAAK1Nke1h=J5KRsSJhjrBgZHXq8HGhFsnaiaqim_xYkgCQ5dNQ@mail.gmail.com>
References: <CAAK1Nke1h=J5KRsSJhjrBgZHXq8HGhFsnaiaqim_xYkgCQ5dNQ@mail.gmail.com>
Message-ID: <7160d56e12bba.5016bd76@johnshopkins.edu>

It seemed that you used a 181x217x181 image as the template when you applied an inverse AIR file. Please use a 128x128x28 image as the template instead.

Xin 


----- Original Message -----
From: Jeff Sadino <jsadino.queens at gmail.com>
Date: Monday, July 30, 2012 2:48 pm
Subject: [Mristudio-users] Inverse Linear Transforms
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Hello,
>  
>  When I apply an inverse linear transform, I would like the Type II 
> ROI map
>  to go from 181x217x181 to 128x128x28.  What happens is that the ROI part
>  does get shrunk down, but the image gets zero-padded and remains at
>  181x217x181.  Is this normal behavior?  Is there any way to shrink the
>  actual dimensions of the ROI map down to 128x128x28?
>  
>  Thank You,
>  Jeff Sadino 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From xli16 at jhmi.edu  Mon Jul 30 17:08:44 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Mon, 30 Jul 2012 17:08:44 -0400
Subject: [Mristudio-users] MultiChannel LDDMM
In-Reply-To: <CAAK1NkdxuNFaUx9t2GCJEoi0xUzHw-+775_Y3FsixDcsqN3+ew@mail.gmail.com>
References: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>
	<CAAK1NkdxuNFaUx9t2GCJEoi0xUzHw-+775_Y3FsixDcsqN3+ew@mail.gmail.com>
Message-ID: <7090e82e1654f.5016bf9c@johnshopkins.edu>

You can submit more than two channel images.



Xin

----- Original Message -----
From: Jeff Sadino <jsadino.queens at gmail.com>
Date: Monday, July 30, 2012 4:47 pm
Subject: Re: [Mristudio-users] MultiChannel LDDMM
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> PS: Minus the Color image because that cannot be converted to Byte format.
>  
>  On Mon, Jul 30, 2012 at 10:42 AM, Jeff Sadino <jsadino.queens at gmail.com>wrote:
>  
>  > Hello,
>  >
>  > I am wondering why we only submit the FA and the Trace images.  It 
> seems
>  > like we could submit the FA, Color, DWI, and Trace images.  I see 
> that the
>  > information from these images come from the same "primary channel", 
> but in
>  > my testing, the more images I submit, the better registration I 
> get.  Is
>  > there anything wrong with submitting all four of these channels?
>  >
>  > Thank You,
>  > Jeff Sadino
>  > 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From susumu at mri.jhu.edu  Mon Jul 30 19:12:12 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 30 Jul 2012 19:12:12 -0400
Subject: [Mristudio-users] MultiChannel LDDMM
In-Reply-To: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>
References: <CAAK1Nkebz-1CcZOpq2Jj+rY7Y62DeCoUVnSXWDAkZPWbpKDn0w@mail.gmail.com>
Message-ID: <CAEq9apKyHdGnNaRq44K4H=02X2i4pET_u+bo3tEsDVC2tg02cg@mail.gmail.com>

Hi Jeff,

I think you can submit up to 4 or 5 channel LDDMM through DiffeoMap.

When you use more channels, the more memory it takes and could take longer
time for calculation. So you want to use the channels wisely. For example,
b0 and trace have very similar contrasts and won't improve the registration
that much. FA+Trace+b0 could put more weight on Trace/b0 contrasts but
other than that, the result should not be much different from FA+Trace. DWI
may provide some additional information and could improve the results. What
we often do is to submit 1/0 binary masking data for the ventricle. This
improves the registration a lot especially for patients with very enlarged
ventricles. This method, however, requires some additional work to define
ventricles.

Addition three channels of color images (red, green, and blue) is another
option. This theoretically allows us to match red fibers to red fibers,
green to green, and blue to blue, further improving the registration, but
there are a couple of things that require attentions. First, strictly
speaking, the fiber color can change due to transformation. Therefore, we
need to generate new color maps after each finite transformation. This
algorithm is not implemented in the current DiffeoMap. Second, red-to-red
matching sounds good for core white matter regions but for peripheral white
matter regions where R, G, B are mixed in a complex and in-reproducible
manner, you may not want to force red-to-red matching.

So,  it is not an easy task to find if addition of new contrasts really
improve registration in a reproducible way. It could also depend on the
amount and nature of the anatomical abnormality of your patient group.  So
I would encourage you to give some testing. Oh, one thing I want to add is,
if you use the color maps with the current DiffeoMap algorithm, you may get
some unhappy reviewers when you submit a paper, although, I believe one of
the original papers in this topic by C.F. Westin used this type of
simplified version of color-to-color registration.


On Mon, Jul 30, 2012 at 4:42 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello,
>
> I am wondering why we only submit the FA and the Trace images.  It seems
> like we could submit the FA, Color, DWI, and Trace images.  I see that the
> information from these images come from the same "primary channel", but in
> my testing, the more images I submit, the better registration I get.  Is
> there anything wrong with submitting all four of these channels?
>
> Thank You,
> Jeff Sadino
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Tue Jul 31 13:31:47 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 31 Jul 2012 13:31:47 -0400
Subject: [Mristudio-users] gradient table
In-Reply-To: <0c898f4d00344bd364a6b97bc87333bf.squirrel@mail.sums.ac.ir>
References: <0c898f4d00344bd364a6b97bc87333bf.squirrel@mail.sums.ac.ir>
Message-ID: <CAEq9apK4cSS0XXoohOKr1n-fUYcBP3Pj6zwO6EjLPcXfPP3Sxg@mail.gmail.com>

The gradient table may change depending on the version of the operating
system, but here is what I have.
You have to modify it to the DtiStudio format.
If you have MOSAIC data, then the easiest way is to use the function to
extract the gradient information in the initial opening window.
If you use only the initial 64 rows of this 256-orientation table, I assume
that you can just use the first 64 rows of this table for tensor
calculations.



---------------------------------------------

  (0,  0.059010, -0.013002,  0.998173);

          (1,  0.070008,  0.157018,  0.985111);

          (2, -0.078038,  0.083041,  0.993486);

          (3, -0.092987, -0.086988,  0.991860);

          (4,  0.046987, -0.178952,  0.982735);

          (5,  0.199944, -0.108970,  0.973729);

          (6,  0.211021,  0.052005,  0.976097);

          (7,  0.210999,  0.212999,  0.953997);

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          (255, -0.380935, -0.922844,  0.056990);

On Fri, Jul 27, 2012 at 3:25 AM, <farshidfar at sums.ac.ir> wrote:

> Hello all
> could you do me a fovour, if someone has gradient table for
> Siemense,Aspino,1.5 tesla with 256 independent gradient directions,would
> it be possible to send it to me. And do you know that if i used only 64
> gradient directions of 256,how can i use this gradient table?
> Thank you so much.
> regards
>
>
> -----------------------------------------
> This email was sent using SquirrelMail.
>    "Webmail for nuts!"
> http://squirrelmail.org/
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From ashley.saito at gmail.com  Fri Aug  3 21:47:01 2012
From: ashley.saito at gmail.com (Ashley Saito)
Date: Fri, 03 Aug 2012 15:47:01 -1000
Subject: [Mristudio-users] Pediatric atlas question
Message-ID: <CAEOhkOT9UidR7WJ3Gzgcc7dZ=eo__cMeLNTk8KYmufx8pOjJfw@mail.gmail.com>

Hello,

My name is Ashley and I am a medical student working with Dr. Chang to
analyze some of her pediatric DTI data. We have subjects between 3-9 years
of age, and were wondering which atlas you would recommend using. Should we
use the 24month pediatric atlas off of http://cmrm.med.jhmi.edu/ or the
standard talairach single subject atlas? Alternatively, could we use age
specific single subjects off of http://cmrm.med.jhmi.edu/ new pediatric dti
data set page? Your input would be greatly appreciated.

Thank you!
Ashley
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From susumu at mri.jhu.edu  Sat Aug  4 16:12:30 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 04 Aug 2012 16:12:30 -0400
Subject: [Mristudio-users] Pediatric atlas question
In-Reply-To: <CAEOhkOT9UidR7WJ3Gzgcc7dZ=eo__cMeLNTk8KYmufx8pOjJfw@mail.gmail.com>
References: <CAEOhkOT9UidR7WJ3Gzgcc7dZ=eo__cMeLNTk8KYmufx8pOjJfw@mail.gmail.com>
Message-ID: <CAEq9ap+tMr1DXX_FkzrM9n0eAoni5cAfuewYU5TCpkZE_77Hig@mail.gmail.com>

Hi Ashley,

I think there is no easy answer to your question. A required precision of a
tool is always a function of the effect size you are going after.

Our experience tells that once subjects reach 3-4 years, anatomical
differences between pediatric  and adult brains are not much more than
individual variability within adult populations and thus registration
accuracy by using an adult atlas for the pediatric population would be
similar to adult populations.

However, we can always argue that age-dependent atlas would provide more
accurate registration and detect more subtle differences.

Below 24 months, especially below 12 months, the brain anatomy is
significantly different from adults and you need age-matched atlases for
accurate registration.

Susumu

On Fri, Aug 3, 2012 at 9:47 PM, Ashley Saito <ashley.saito at gmail.com> wrote:

> Hello,
>
> My name is Ashley and I am a medical student working with Dr. Chang to
> analyze some of her pediatric DTI data. We have subjects between 3-9 years
> of age, and were wondering which atlas you would recommend using. Should we
> use the 24month pediatric atlas off of http://cmrm.med.jhmi.edu/ or the
> standard talairach single subject atlas? Alternatively, could we use age
> specific single subjects off of http://cmrm.med.jhmi.edu/ new pediatric
> dti data set page? Your input would be greatly appreciated.
>
> Thank you!
> Ashley
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From jjames2 at umc.edu  Tue Aug  7 10:43:35 2012
From: jjames2 at umc.edu (Judy James)
Date: Tue, 07 Aug 2012 14:43:35 +0000
Subject: [Mristudio-users] DTI images from VErio
Message-ID: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>

Dear members,
I have a question about a data set I received from Siemens Verio.
The images are in Mosaic form with 63 sets of 28 images in it. The DICOM header says 20 directions with 1 average. I don't understand how it has 63 sets of mosaic if it was only 20 directions.

Can any one help?
I am also on the look out for the 20 direction gradient table used on Verio. Can any one share it?

Thanks
Judy




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From Uzeyir.Ahmadli at usz.ch  Tue Aug  7 11:04:05 2012
From: Uzeyir.Ahmadli at usz.ch (Ahmadli Uzeyir)
Date: Tue, 07 Aug 2012 15:04:05 +0000
Subject: [Mristudio-users] DTI images from VErio
In-Reply-To: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
Message-ID: <5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>

Dear all,



I have forgot my password for mristudio.org.

Does anyone know how I can get into contact with support team?



Thanks in advance

UA

________________________________

From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Judy James [jjames2 at umc.edu]
Sent: Tuesday, August 07, 2012 16:43
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] DTI images from VErio

Dear members,
I have a question about a data set I received from Siemens Verio.
The images are in Mosaic form with 63 sets of 28 images in it. The DICOM header says 20 directions with 1 average. I don't understand how it has 63 sets of mosaic if it was only 20 directions.

Can any one help?
I am also on the look out for the 20 direction gradient table used on Verio. Can any one share it?

Thanks
Judy



Individuals who have received this information in error or are not authorized to receive it must promptly return or dispose of the information and notify the sender. Those individuals are hereby notified that they are strictly prohibited from reviewing, forwarding, printing, copying, distributing or using this information in any way.


From xli16 at jhmi.edu  Tue Aug  7 15:05:20 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Tue, 07 Aug 2012 15:05:20 -0400
Subject: [Mristudio-users] DTI images from VErio
In-Reply-To: <5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
Message-ID: <7230c5131d2a6.50212eb0@johnshopkins.edu>

Please go to https://www.mristudio.org/register/forgetpassword.php to get your password back.

Xin

----- Original Message -----
From: Ahmadli Uzeyir <Uzeyir.Ahmadli at usz.ch>
Date: Tuesday, August 7, 2012 11:04 am
Subject: Re: [Mristudio-users] DTI images from VErio
To: "DTI Studio, ROI Editor,	DiffeoMap Questions/Support" <mristudio-users at mristudio.org>


> Dear all,
>  
>  
>  
>  I have forgot my password for mristudio.org.
>  
>  Does anyone know how I can get into contact with support team?
>  
>  
>  
>  Thanks in advance
>  
>  UA
>  
>  ________________________________
>  
>  From: mristudio-users-bounces at mristudio.org 
> [mristudio-users-bounces at mristudio.org] on behalf of Judy James [jjames2 at umc.edu]
>  Sent: Tuesday, August 07, 2012 16:43
>  To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>  Subject: [Mristudio-users] DTI images from VErio
>  
>  Dear members,
>  I have a question about a data set I received from Siemens Verio.
>  The images are in Mosaic form with 63 sets of 28 images in it. The 
> DICOM header says 20 directions with 1 average. I don't understand how 
> it has 63 sets of mosaic if it was only 20 directions.
>  
>  Can any one help?
>  I am also on the look out for the 20 direction gradient table used on 
> Verio. Can any one share it?
>  
>  Thanks
>  Judy
>  
>  
>  
>  Individuals who have received this information in error or are not 
> authorized to receive it must promptly return or dispose of the 
> information and notify the sender. Those individuals are hereby 
> notified that they are strictly prohibited from reviewing, forwarding, 
> printing, copying, distributing or using this information in any way.
>  
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From lujiaoluo1990 at 126.com  Thu Aug  9 08:07:02 2012
From: lujiaoluo1990 at 126.com (=?GBK?B?wt7otL2/?=)
Date: Thu, 09 Aug 2012 20:07:02 +0800 (CST)
Subject: [Mristudio-users] dti  roi problem
In-Reply-To: <7230c5131d2a6.50212eb0@johnshopkins.edu>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
	<7230c5131d2a6.50212eb0@johnshopkins.edu>
Message-ID: <4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>

Dear all,
  It's my first time to process  dti datas, and I am puzzled by how to draw a roi on a diffusion image.
  I am wondering that how to select precisely the anatomical structures you want to analyze (e.g. amygdala, FFA, and V1)  on a diffusion data? What should I do with dtistudio? Or do I need to look for some other softwares?
 
Looking forward for your help and thanks so much!




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From susumu at mri.jhu.edu  Thu Aug  9 08:36:17 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 09 Aug 2012 08:36:17 -0400
Subject: [Mristudio-users] dti roi problem
In-Reply-To: <4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
	<7230c5131d2a6.50212eb0@johnshopkins.edu>
	<4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>
Message-ID: <CAEq9ap+149GHsJQzH6xxChn6RKGBud1DkB7cB4TBkEcnCsNwVQ@mail.gmail.com>

Your question have two parts;

1) How to use the software to draw ROI: The ROI drawing function of
DtiStudio is limited. I would suggest you to download RoiEditor from
www.mristudio.org, which has more advanced ROI drawing functions.
2) How to anatomically define structures: White matter structures can be
better identified by FA and color-coded maps. For gray matter structures,
it depends. For the cortex, DTI may not have enough resolution to define
it. Structures such as the caudate, thalamus, hippo, amyg could be better
defined by b0 and diffusion-weighted images than FA.

You may want to learn automated segmentation tools using DiffeoMap and
RoiEditor in www.mristudio.org, which can incorporate both FA and b0 images
to define many brain structures automatically.

Susumu

On Thu, Aug 9, 2012 at 8:07 AM, ??? <lujiaoluo1990 at 126.com> wrote:

> Dear all,
>   It's my first time to process  dti datas, and I am puzzled by how to
> draw a roi on a diffusion image.
>   I am wondering that how to select precisely the anatomical structures
> you want to analyze (e.g. amygdala, FFA, and V1)  on a diffusion data? What
> should I do with dtistudio? Or do I need to look for some other softwares?
>
> Looking forward for your help and thanks so much!
>
>
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From ycq0565 at 126.com  Thu Aug  9 09:38:02 2012
From: ycq0565 at 126.com (ycq0565)
Date: Thu, 09 Aug 2012 21:38:02 +0800 (CST)
Subject: [Mristudio-users] FA and MD problem
In-Reply-To: <4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
	<7230c5131d2a6.50212eb0@johnshopkins.edu>
	<4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>
Message-ID: <18be65e2.10b8a.1390b9b2c12.Coremail.ycq0565@126.com>

Dear all,
  I am using DTI-studio to measure the FA and MD values of caudate head and putamen, but when I put the ROIs on them in fibertracking panel, I can't obtain a value,  and it's just show N/A. Can anyone show me the steps in detail on how to do this work?
Looking forward for your help and thanks very much!




 


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From susumu at mri.jhu.edu  Thu Aug  9 11:58:12 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 09 Aug 2012 11:58:12 -0400
Subject: [Mristudio-users] FA and MD problem
In-Reply-To: <18be65e2.10b8a.1390b9b2c12.Coremail.ycq0565@126.com>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<5C1876F4495A834CAE74C35EE218C38E4EFDA33E@DS-00520.usz.ch>
	<7230c5131d2a6.50212eb0@johnshopkins.edu>
	<4509d246.a75c.1390b47dab8.Coremail.lujiaoluo1990@126.com>
	<18be65e2.10b8a.1390b9b2c12.Coremail.ycq0565@126.com>
Message-ID: <CAEq9ap+3FrG3GYLAOCB+_ST-kP-JsE3NEVKu-K2Rr9mFtigsVQ@mail.gmail.com>

I think the best way to start is the video tutorial at
https://www.mristudio.org/documentation/video/MristudioTutorialVideo/index.htm
.

The data used in this video tutorial can also be downloaded from the
"Workshop" section of www.mristudio.org.

On Thu, Aug 9, 2012 at 9:38 AM, ycq0565 <ycq0565 at 126.com> wrote:

> Dear all,
>
>   I am using DTI-studio to measure the FA and MD values of caudate head
> and putamen, but when I put the ROIs on them in fibertracking panel, I
> can't obtain a value,  and it's just show N/A. Can anyone show me the steps
> in detail on how to do this work?
> Looking forward for your help and thanks very much!
>
>
>
>
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From lujiaoluo1990 at 126.com  Mon Aug 13 01:18:04 2012
From: lujiaoluo1990 at 126.com (=?GBK?B?wt7otL2/?=)
Date: Mon, 13 Aug 2012 13:18:04 +0800 (CST)
Subject: [Mristudio-users] dtistudio import data
Message-ID: <12b3c42a.780c.1391e6adfbb.Coremail.lujiaoluo1990@126.com>

Dear all, I would like to consult you a problem.

  I had use the dtistudio to process our dti data. Our data were obtained from Simens 3T with 31 volumes (30 directions). But when I imported the data(31 volumes) into dtistudio, it can only display one 2D image on the 3D viewer pane, and can only display the axial view? Is there something wrong with my data? What can I do import the correct data and images?

Thanks so much!
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From rajagov2 at ccf.org  Tue Aug 14 16:53:40 2012
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Tue, 14 Aug 2012 16:53:40 -0400
Subject: [Mristudio-users] A clarification on the statistics table
Message-ID: <190A50FE6C374841B0D466F13F96987C555670@CCHSCLEXMB80.cc.ad.cchs.net>

Dear All,
 
I am calculating changes in FA and other DTI metrics along CST. After tract reconstruction I use statistics option to see FA/other DTI metrics values. The statistics gives me Max, Min, Mean, SD values in each and every slice in my image volume. I am wondering whether I can use Max, value (or only mean has to be used) to study changes between my control and patients.
 
Thanks
Venkat

===================================


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law.  If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited.  If you have received this communication in error,  please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.  

Thank you.
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From akalanu1 at jhmi.edu  Tue Aug 14 17:27:07 2012
From: akalanu1 at jhmi.edu (Atul Kalanuria)
Date: Tue, 14 Aug 2012 21:27:07 +0000
Subject: [Mristudio-users] A clarification on the statistics table
In-Reply-To: <190A50FE6C374841B0D466F13F96987C555670@CCHSCLEXMB80.cc.ad.cchs.net>
References: <190A50FE6C374841B0D466F13F96987C555670@CCHSCLEXMB80.cc.ad.cchs.net>
Message-ID: <B3E8AB496CFCD443B197F884DFEED3791205586E@JHEMTMWEX6.win.ad.jhu.edu>

I would use mean values.

Atul.
On Aug 14, 2012, at 4:53 PM, "Rajagopalan, Venkateswaran" <rajagov2 at ccf.org<mailto:rajagov2 at ccf.org>>
 wrote:

Dear All,

I am calculating changes in FA and other DTI metrics along CST. After tract reconstruction I use statistics option to see FA/other DTI metrics values. The statistics gives me Max, Min, Mean, SD values in each and every slice in my image volume. I am wondering whether I can use Max, value (or only mean has to be used) to study changes between my control and patients.

Thanks
Venkat

===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

_______________________________________________
mristudio-users mailing list
mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org


From rajagov2 at ccf.org  Wed Aug 15 11:05:46 2012
From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran)
Date: Wed, 15 Aug 2012 11:05:46 -0400
Subject: [Mristudio-users] A clarification on the statistics table
Message-ID: <190A50FE6C374841B0D466F13F96987C555677@CCHSCLEXMB80.cc.ad.cchs.net>

Thanks, Is it ok to take the mean of this mean value (if the data meets assumptions of t-test and you want to do t-test) across subjects when you perform stats
 
Thanks
Venkat
 
 
 
I would use mean values.

Atul.
On Aug 14, 2012, at 4:53 PM, "Rajagopalan, Venkateswaran" <rajagov2 at ccf.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users> <mailto:rajagov2 at ccf.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users> >>
wrote:

Dear All,

I am calculating changes in FA and other DTI metrics along CST. After tract reconstruction I use statistics option to see FA/other DTI metrics values. The statistics gives me Max, Min, Mean, SD values in each and every slice in my image volume. I am wondering whether I can use Max, value (or only mean has to be used) to study changes between my control and patients.

Thanks
Venkat



===================================


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law.  If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited.  If you have received this communication in error,  please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.  

Thank you.
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From raviteja.kotikalapudi at gmail.com  Wed Aug 15 12:03:04 2012
From: raviteja.kotikalapudi at gmail.com (Kotikalapudi Raviteja)
Date: Wed, 15 Aug 2012 17:03:04 +0100
Subject: [Mristudio-users] A clarification on the statistics table
In-Reply-To: <190A50FE6C374841B0D466F13F96987C555677@CCHSCLEXMB80.cc.ad.cchs.net>
References: <190A50FE6C374841B0D466F13F96987C555677@CCHSCLEXMB80.cc.ad.cchs.net>
Message-ID: <CAGJ50wY8ZwUNGH-_pcBjJSLQV2W-SM1qfnFuaL1aey+__HPBBQ@mail.gmail.com>

Hi Venkat,

I would suggest you to have a look at the Median Values as well. As they
are less effected by the Min and Max values. They could be quite helpful
for your statistical analysis. It should be fine if you consider averaging
the mean values for your t-test results.

---KRT

On Wed, Aug 15, 2012 at 4:05 PM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

>  Thanks, Is it ok to take the mean of this mean value (if the data
> meets assumptions of t-test and you want to do t-test) across subjects when
> you perform stats
>
> Thanks
> Venkat
>
>
>
> I would use mean values.
>
> Atul.
> On Aug 14, 2012, at 4:53 PM, "Rajagopalan, Venkateswaran" <rajagov2 at
> ccf.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> <mailto:rajagov2 at ccf.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> >>
> wrote:
>
> Dear All,
>
> I am calculating changes in FA and other DTI metrics along CST. After
> tract reconstruction I use statistics option to see FA/other DTI metrics
> values. The statistics gives me Max, Min, Mean, SD values in each and every
> slice in my image volume. I am wondering whether I can use Max, value (or
> only mean has to be used) to study changes between my control and patients.
>
> Thanks
> Venkat
>
> ===================================
>
> Please consider the environment before printing this e-mail****
> Cleveland Clinic is ranked one of the top hospitals in America by U.S.News
> & World Report (2010). Visit us online at http://www.clevelandclinic.orgfor a complete listing of our services, staff and locations.
> Confidentiality Note: This message is intended for use only by the
> individual or entity to which it is addressed and may contain information
> that is privileged, confidential, and exempt from disclosure under
> applicable law. If the reader of this message is not the intended recipient
> or the employee or agent responsible for delivering the message to the
> intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From cyrus at vtc.vt.edu  Wed Aug 15 14:32:46 2012
From: cyrus at vtc.vt.edu (Cyrus Eierud)
Date: Wed, 15 Aug 2012 18:32:46 +0000
Subject: [Mristudio-users] ICBM-81 complement for FMi and FMa?
Message-ID: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB82C9@gellar.vtcri.local>

Dear MRI Studio,

Thanks for your great class in July!
Working with a meta analysis of WM regions I decided to use the ICBM-81 as the gold standard, which all other articles has to match even if coordinates are used. However, ICBM-81 does not include the important forceps minor (FMi) nor forceps major (FMa) regions. I found that in FSL there are JHU-ICBM-tracts-maxprob-thr0-1mm.nii, JHU-ICBM-tracts-maxprob-thr25-1mm.nii and JHU-ICBM-tracts-maxprob-thr50-1mm.nii that do include both FMi and FMa, but with different thresholds. I thought I could create my own map by merging one of the other 3 maps with the ICBM-81, but I would like FMi and FMa to have a comparable threshold to the original threshold of ICBM-81. In my study I need the parcellated spatial ROI distributions to have the same threshold (including for FMi and FMa). Can you recommend which FMi/FMa map I should use to merge with the ICBM-81 to get a complete white matter parcellation map? In addition, I don't necessarily need to merge the additional map to the ICBM-81. It is also okay if you tell me which map, which includes FMi and FMa, that has the most comparable threshold as the ICBM-81 map.

Best Regards,
Cyrus Eierud
Graduate student in the LaConte Lab
Baylor College of Medicine, TX and
Virginia Tech Carilion Research Institute




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From susumu at mri.jhu.edu  Wed Aug 15 15:15:25 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 15 Aug 2012 15:15:25 -0400
Subject: [Mristudio-users] A clarification on the statistics table
In-Reply-To: <190A50FE6C374841B0D466F13F96987C555677@CCHSCLEXMB80.cc.ad.cchs.net>
References: <190A50FE6C374841B0D466F13F96987C555677@CCHSCLEXMB80.cc.ad.cchs.net>
Message-ID: <CAEq9apJQjXPERACpDDKeMa9oKexvi8SNiPDatzZo345w57iShw@mail.gmail.com>

Hi Venkat,

I think you can use the mean value to compare across people.

As you may already know, you can get two types of reports; an overall mean
of all pixels in the 3D tract volume and the slice-by-slice report. It the
tract of your interest, in your case CST, travels linearly and is more or
less perpendicular to one of the planes (for CST, it is perpendicular to
axial slices), the slice-by-slice report would be informative. If you use
the whole-tract report, not the slice-by-slice, you may also want to try
some metrics other than the overall mean, such as median (as KRT suggested)
or histogram. You can save the tract as a raw 3D file, load it to RoiEditor
as an object, also load an FA map, apply the object as an ROI to the FA
map, and then you can save FA values of all individual pixels in the object
(ROI), from which you can create a histogram by Excel. This could be an
interesting approach for fibers like corpus callosum, uncinate, or SLF,
which make a large turn and slice-by-slice report may not be a good idea.

When you use slice-by-slice report, you have to normalize the slice
locations across subjects. For example, the CST at pons could be slice #12
in Subject A and #15 in Subject B. The total length of the CST of Subject
#A could be 35 slices while that of Subject #b could be 38 slices. This
requires "spatial normalization".

What we did in old days is, load all slice-by-slice reports from multiple
subjects to an Excel sheet, slide the whole column up and down to make sure
that the CST at the pons of all subjects align in the Excel sheet. This is
the same as rigid translation to adjust the slice locations. Even if the
CST locations are now aligned at the pons level, This doesn't guarantee
that the CST is aligned in the motor cortex because the CST lengths are
different among subjects. Then you can stretch or shrink the Excel column
of each subject so that everybody has the same column length. This is the
same as linear alignment using two-point scaling.

While all the location normalization is performed using Excel in this
example, you can also do image normalization in the imaging domain. For
this, you need to use DiffeoMap (or other kinds of brain normalization
software such as SPM and FSL). You can do fiber tracking in the native
data. Then linearly normalize all subject data to the MNI space, from which
you can get slice-by-slice report in a normalized manner. All slice
locations and fiber lengths are the same in Excel, without further
modifications.

You can also do normalization of images first to the MNI space and then do
fiber tracking in the MNI space. If you want to do this, you have to
normalize your tensor data.

If we push this logic further, then we can ask, "do we need tractography?".

> Suppose one location of CST, say, at the cerebral peduncle (CP) level, is
affected and has low FA values in a patient population.

> If we do CST tracking and get an overall averaged FA, we can say, "it's
not a sensitive way because we mix all pixels from other normal locations".
This is a valid logic.

>Then we say, "ok, let's look at slice-by-slice report. This should show
low FA at the CP level." The only problem is, the CP level slices are not
consistent across subjects. So, for each subject, we have to identify slice
#. To make sure that the low FA happens only at CP, we want to compare FAs
at pons level, internal capsule level, corona radiata level, etc. Then we
have to identify slice # of these multiple locations for all subjects.
That's a lot of work.

> So, what we usually do is to use one of the image "normalization" tools
that can adjust the location, rotation, and size of the brain across
subjects. Then all slice levels are the same. We can do slice-by-slice
comparison across subjects.

> Well, however, if all brains are well normalized, we can do
voxel-by-voxel comparison across subjects without fiber tracking. If
patient populations have consistently low FA at the CP, the voxel-by-voxel
comparison should show it anyway. This is the logic for voxel-based
analysis (VBA), which is a widely used technique.

> There could be two reasons why you want to use tractography over VBA.
First, VBA always have normalization error. In this case, if the CP
structures are not well aligned after normalization, we may fail to detect
the FA loss. Using tractography in each subject, we know that we are
accurately comparing CST vs CST (or CP vs CP). In this sense, we can call
tractography a "registration tool", with which we can define voxels that
belong to the CST in all subjects accurately. Another point is that
tractography groups pixels. If the grouped pixels share the same property,
such as reduced FA, it can provide much higher SNR compared to
voxel-by-voxel comparison. In this sense, you can call tractography a
"spatial filter". SNR is always a problem in VBA and we usually group
pixels using isotropic filters. Tractography is a structure-specific
spatial filter.

> One counter argument is, tractography is not a stable operation. It
requires subjective ROI delineation. Also, it is sensitive to noise; if you
scan the same patient twice, the tractography results are not the same. So
there is a downside of tractography. This is a precision (reliability)
issue.

> Another approach we often use is Atlas-based analysis (ABA), which is
also based on the whole brain normalization, followed by whole-brain
segmentation by applying a pre-defined segmentation file. This pre-defined
segmentation file is another kind of structure-specific spatial filter,
defining which pixels should be grouped.

> These methods are all related and have pros & cons.

Hope this gives you a big picture about DTI data analysis.

Susumu



On Wed, Aug 15, 2012 at 11:05 AM, Rajagopalan, Venkateswaran <
rajagov2 at ccf.org> wrote:

>  Thanks, Is it ok to take the mean of this mean value (if the data
> meets assumptions of t-test and you want to do t-test) across subjects when
> you perform stats
>
> Thanks
> Venkat
>
>
>
> I would use mean values.
>
> Atul.
> On Aug 14, 2012, at 4:53 PM, "Rajagopalan, Venkateswaran" <rajagov2 at
> ccf.org <http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> <mailto:rajagov2 at ccf.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
> >>
> wrote:
>
> Dear All,
>
> I am calculating changes in FA and other DTI metrics along CST. After
> tract reconstruction I use statistics option to see FA/other DTI metrics
> values. The statistics gives me Max, Min, Mean, SD values in each and every
> slice in my image volume. I am wondering whether I can use Max, value (or
> only mean has to be used) to study changes between my control and patients.
>
> Thanks
> Venkat
>
> ===================================
>
> Please consider the environment before printing this e-mail****
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From susumu at mri.jhu.edu  Wed Aug 15 15:34:34 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 15 Aug 2012 15:34:34 -0400
Subject: [Mristudio-users] ICBM-81 complement for FMi and FMa?
In-Reply-To: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB82C9@gellar.vtcri.local>
References: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB82C9@gellar.vtcri.local>
Message-ID: <CAEq9ap+8+Wx=oAAvXCEGwyEV-cnk=9vOQrhZpc5FA+vhQ8O7uw@mail.gmail.com>

Hi Cyrus,

When we parcellate the white matter, there are two different approaches.
This is somewhat similar to geological maps, which also contain two types
of information. One is location boarders and the other is road maps. For
example, City of Baltimore or Maryland State are defined by boarders. On
the other hand Route 40 penetrates multiple cities and states.

Our parcellation maps (WMPM) are similar to the location boarders. Based on
image contrasts, we tried to define structures. If we look at the posterior
limb of the internal capsule, we can define it based on FA contrasts
(differentiate it from thalamus and putamen), color (fiber orientation,
differentiate it from the anterior limb and retrolenticular internal
capsule), and anatomical landmarks. We also have white matter definitions
based on tractography, which is similar to the road map in the above
analogy. The corticospinal tract penetrates the pons, a portion of the
posterior limb of the internal capsule, and the corona radiata.

For FMi and FMa, they are divided into several portions in our WMPM.
However, I believe that FMi and FMa are a part of the fibers provided in
"Tracts" option in the "Atlas" section of the right column of RoiEditor.
Please select "JHU_MNI_GA" as the atlas in the "Atlas" section and click
"open" in the "Tract" section. You can load and look at the
population-probabilistic locations. They are generated from JHU DTI data,
but the coordinates are quite compatible with ICBM-MNI. In the RoiEditor
directory, you can also find the 3D raw files of these fibers.

Susumu

On Wed, Aug 15, 2012 at 2:32 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:

>  Dear MRI Studio,
>
>  Thanks for your great class in July!
> Working with a meta analysis of WM regions I decided to use the ICBM-81 as
> the gold standard, which all other articles has to match even if
> coordinates are used. However, ICBM-81 does not include the important
> forceps minor (FMi) nor forceps major (FMa) regions. I found that in FSL
> there are JHU-ICBM-tracts-maxprob-thr0-1mm.nii,
> JHU-ICBM-tracts-maxprob-thr25-1mm.nii and
> JHU-ICBM-tracts-maxprob-thr50-1mm.nii that do include both FMi and FMa, but
> with different thresholds. I thought I could create my own map by merging
> one of the other 3 maps with the ICBM-81, but I would like FMi and FMa to
> have a comparable threshold to the original threshold of ICBM-81. In my
> study I need the parcellated spatial ROI distributions to have the same
> threshold (including for FMi and FMa). Can you recommend which FMi/FMa map
> I should use to merge with the ICBM-81 to get a complete white matter
> parcellation map? In addition, I don't necessarily need to merge the
> additional map to the ICBM-81. It is also okay if you tell me which map,
> which includes FMi and FMa, that has the most comparable threshold as the
> ICBM-81 map.
>
>    Best Regards,
>  Cyrus Eierud
> Graduate student in the LaConte Lab
> Baylor College of Medicine, TX and
> Virginia Tech Carilion Research Institute
>
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From cyrus at vtc.vt.edu  Wed Aug 15 13:56:37 2012
From: cyrus at vtc.vt.edu (Cyrus Eierud)
Date: Wed, 15 Aug 2012 17:56:37 +0000
Subject: [Mristudio-users] Can't post messages on MRI Studio Forum
Message-ID: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB829A@gellar.vtcri.local>

Dear MRIStudio,

I'm an MRI-Studio user who would like to post a question about the ICBM-81. However, I am not allowed to log in to the forum and therefore can't post anything. I try to log in in two ways. First,  I try my MRIStudio user, which I have access to since I can log in and edit my account at www.mristudio.org (resulting in attachment). However, same user and password can not log into the forum area, which I want in order to ask my question. Secondly, I tried to create a new user from the forum page, but when the password that is supposed to be emailed I never get. I have checked my spam folder that did not receive any email either.

Can you help out so I can log in and post a message?

Best Regards,
Cyrus Eierud
Graduate student in the LaConte Lab
Baylor College of Medicine, TX and
Virginia Tech Carilion Research Institute
Mobile (540) 314-6449
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From cyrus at vtc.vt.edu  Thu Aug 16 15:29:15 2012
From: cyrus at vtc.vt.edu (Cyrus Eierud)
Date: Thu, 16 Aug 2012 19:29:15 +0000
Subject: [Mristudio-users] ICBM-81 complement for FMi and FMa?
In-Reply-To: <CAEq9ap+8+Wx=oAAvXCEGwyEV-cnk=9vOQrhZpc5FA+vhQ8O7uw@mail.gmail.com>
References: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB82C9@gellar.vtcri.local>
	<CAEq9ap+8+Wx=oAAvXCEGwyEV-cnk=9vOQrhZpc5FA+vhQ8O7uw@mail.gmail.com>
Message-ID: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB88E0@gellar.vtcri.local>

Susumo,

Thanks for your clear explanations about the core probability tract maps. Using the ROIEditor I selected and thresholded my ROIs (FMi and FMa) for everything between 0.001 to 1 (resulting in an acceptance of any probability above zero) to depict the ROIs. This result also matched the FMi and FMa from your JHU-ICBM-tracts-maxprob-thr0-1mm.nii, from FSL, with the exception that the result from the ROIEditor concistently had approximately 2% more voxels by the ROIs borders. This greatly answers the question about which tract map to use, where the ROIEditor seems to be the gold standard. May I ask a follow up question that if my (arbitrarily chosen) threshold (0.001 to 1) really is the best match to the threshold used in the ICBM-DTI-81 atlas?

Best Regards,
Cyrus
________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of susumu mori [susumu at mri.jhu.edu]
Sent: Wednesday, August 15, 2012 3:34 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] ICBM-81 complement for FMi and FMa?

Hi Cyrus,

When we parcellate the white matter, there are two different approaches. This is somewhat similar to geological maps, which also contain two types of information. One is location boarders and the other is road maps. For example, City of Baltimore or Maryland State are defined by boarders. On the other hand Route 40 penetrates multiple cities and states.

Our parcellation maps (WMPM) are similar to the location boarders. Based on image contrasts, we tried to define structures. If we look at the posterior limb of the internal capsule, we can define it based on FA contrasts (differentiate it from thalamus and putamen), color (fiber orientation, differentiate it from the anterior limb and retrolenticular internal capsule), and anatomical landmarks. We also have white matter definitions based on tractography, which is similar to the road map in the above analogy. The corticospinal tract penetrates the pons, a portion of the posterior limb of the internal capsule, and the corona radiata.

For FMi and FMa, they are divided into several portions in our WMPM. However, I believe that FMi and FMa are a part of the fibers provided in "Tracts" option in the "Atlas" section of the right column of RoiEditor. Please select "JHU_MNI_GA" as the atlas in the "Atlas" section and click "open" in the "Tract" section. You can load and look at the population-probabilistic locations. They are generated from JHU DTI data, but the coordinates are quite compatible with ICBM-MNI. In the RoiEditor directory, you can also find the 3D raw files of these fibers.

Susumu

On Wed, Aug 15, 2012 at 2:32 PM, Cyrus Eierud <cyrus at vtc.vt.edu<mailto:cyrus at vtc.vt.edu>> wrote:
Dear MRI Studio,

Thanks for your great class in July!
Working with a meta analysis of WM regions I decided to use the ICBM-81 as the gold standard, which all other articles has to match even if coordinates are used. However, ICBM-81 does not include the important forceps minor (FMi) nor forceps major (FMa) regions. I found that in FSL there are JHU-ICBM-tracts-maxprob-thr0-1mm.nii, JHU-ICBM-tracts-maxprob-thr25-1mm.nii and JHU-ICBM-tracts-maxprob-thr50-1mm.nii that do include both FMi and FMa, but with different thresholds. I thought I could create my own map by merging one of the other 3 maps with the ICBM-81, but I would like FMi and FMa to have a comparable threshold to the original threshold of ICBM-81. In my study I need the parcellated spatial ROI distributions to have the same threshold (including for FMi and FMa). Can you recommend which FMi/FMa map I should use to merge with the ICBM-81 to get a complete white matter parcellation map? In addition, I don't necessarily need to merge the additional map to the ICBM-81. It is also okay if you tell me which map, which includes FMi and FMa, that has the most comparable threshold as the ICBM-81 map.

Best Regards,
Cyrus Eierud
Graduate student in the LaConte Lab
Baylor College of Medicine, TX and
Virginia Tech Carilion Research Institute





_______________________________________________
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From susumu at mri.jhu.edu  Thu Aug 16 17:27:35 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 16 Aug 2012 17:27:35 -0400
Subject: [Mristudio-users] ICBM-81 complement for FMi and FMa?
In-Reply-To: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB88E0@gellar.vtcri.local>
References: <DBF07F512FBA894E8B902EDBF9A3DB2F08FB82C9@gellar.vtcri.local>
	<CAEq9ap+8+Wx=oAAvXCEGwyEV-cnk=9vOQrhZpc5FA+vhQ8O7uw@mail.gmail.com>
	<DBF07F512FBA894E8B902EDBF9A3DB2F08FB88E0@gellar.vtcri.local>
Message-ID: <CAEq9apJgOe1SD02Oc2LEAP=KyVvmkK_e6d=0_2rVdo1Q4cehnQ@mail.gmail.com>

Hi Cyrus,

I think we really can't argue which threshold is right and which is wrong.
This is just a matter of pick one and use the same criteria for all
subjects. One thing you should worry about is the sensitivity of your final
results on the arbitrary chosen threshold.

Another approach I could recommend is, instead of applying a hard threshold
and convert the probability map to 1/0 masking map (basically, you applied
a cut off filter), you can apply the population-probability weighting. For
example, suppose you have two pixels; one has probability 0.8 and the other
has 0.5. Also, suppose the first pixel has FA = 0.6 and second one has FA =
0.4. If you use the hard cut-off, you get (0.6+0.4)/2 for FA report. If you
use the probability weighting, you get [0.6 (FA) x 0.8 (probability) + 0.4
x 0.5]/[0.8+0.5]. In this way, you get FA values weighted by probability.
This function is already built in RoiEditor.

On Thu, Aug 16, 2012 at 3:29 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:

>  Susumo,
>
> Thanks for your clear explanations about the core probability tract maps.
> Using the ROIEditor I selected and thresholded my ROIs (FMi and FMa) for
> everything between 0.001 to 1 (resulting in an acceptance of any
> probability above zero) to depict the ROIs. This result also matched the
> FMi and FMa from your JHU-ICBM-tracts-maxprob-thr0-1mm.nii, from FSL, with
> the exception that the result from the ROIEditor concistently had
> approximately 2% more voxels by the ROIs borders. This greatly answers the
> question about which tract map to use, where the ROIEditor seems to be the
> gold standard. May I ask a follow up question that if my (arbitrarily
> chosen) threshold (0.001 to 1) really is the best match to the threshold
> used in the ICBM-DTI-81 atlas?
>
> Best Regards,
> Cyrus
>  ------------------------------
> *From:* mristudio-users-bounces at mristudio.org [
> mristudio-users-bounces at mristudio.org] on behalf of susumu mori [
> susumu at mri.jhu.edu]
> *Sent:* Wednesday, August 15, 2012 3:34 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] ICBM-81 complement for FMi and FMa?
>
>  Hi Cyrus,
>
>  When we parcellate the white matter, there are two different approaches.
> This is somewhat similar to geological maps, which also contain two types
> of information. One is location boarders and the other is road maps. For
> example, City of Baltimore or Maryland State are defined by boarders. On
> the other hand Route 40 penetrates multiple cities and states.
>
>  Our parcellation maps (WMPM) are similar to the location boarders. Based
> on image contrasts, we tried to define structures. If we look at the
> posterior limb of the internal capsule, we can define it based on FA
> contrasts (differentiate it from thalamus and putamen), color (fiber
> orientation, differentiate it from the anterior limb and retrolenticular
> internal capsule), and anatomical landmarks. We also have white matter
> definitions based on tractography, which is similar to the road map in the
> above analogy. The corticospinal tract penetrates the pons, a portion of
> the posterior limb of the internal capsule, and the corona radiata.
>
>  For FMi and FMa, they are divided into several portions in our WMPM.
> However, I believe that FMi and FMa are a part of the fibers provided in
> "Tracts" option in the "Atlas" section of the right column of RoiEditor.
> Please select "JHU_MNI_GA" as the atlas in the "Atlas" section and click
> "open" in the "Tract" section. You can load and look at the
> population-probabilistic locations. They are generated from JHU DTI data,
> but the coordinates are quite compatible with ICBM-MNI. In the RoiEditor
> directory, you can also find the 3D raw files of these fibers.
>
>  Susumu
>
> On Wed, Aug 15, 2012 at 2:32 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:
>
>>  Dear MRI Studio,
>>
>>  Thanks for your great class in July!
>> Working with a meta analysis of WM regions I decided to use the ICBM-81
>> as the gold standard, which all other articles has to match even if
>> coordinates are used. However, ICBM-81 does not include the important
>> forceps minor (FMi) nor forceps major (FMa) regions. I found that in FSL
>> there are JHU-ICBM-tracts-maxprob-thr0-1mm.nii,
>> JHU-ICBM-tracts-maxprob-thr25-1mm.nii and
>> JHU-ICBM-tracts-maxprob-thr50-1mm.nii that do include both FMi and FMa, but
>> with different thresholds. I thought I could create my own map by merging
>> one of the other 3 maps with the ICBM-81, but I would like FMi and FMa to
>> have a comparable threshold to the original threshold of ICBM-81. In my
>> study I need the parcellated spatial ROI distributions to have the same
>> threshold (including for FMi and FMa). Can you recommend which FMi/FMa map
>> I should use to merge with the ICBM-81 to get a complete white matter
>> parcellation map? In addition, I don't necessarily need to merge the
>> additional map to the ICBM-81. It is also okay if you tell me which map,
>> which includes FMi and FMa, that has the most comparable threshold as the
>> ICBM-81 map.
>>
>>    Best Regards,
>>  Cyrus Eierud
>> Graduate student in the LaConte Lab
>> Baylor College of Medicine, TX and
>> Virginia Tech Carilion Research Institute
>>
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Thu Aug 16 18:22:10 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 16 Aug 2012 18:22:10 -0400
Subject: [Mristudio-users] DTI images from VErio
In-Reply-To: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
Message-ID: <CAEq9apJ8Yc9S5jRA=0854Z1Q=wFhP7RPX8oOPTo3H31=J8ux1A@mail.gmail.com>

Hi Judy,

I guess you did 3 signal averaging?
In Siemens scanners, the signal averaging doesn't really average the data
and save all scans in separate files. So, you may have 3 repetitions of
1+20.

For the table, please try this;

0:   0, 0, 0
1:   1.000000,  0.000000,  0.000000;
2:   0.000000,  1.000000,  0.000000;
3:  -0.031984,  0.799591,  0.599693;
4:   0.856706,  0.493831, -0.148949;
5:   0.834429,  0.309159,  0.456234;
6:   0.834429, -0.309159,  0.456234;
7:   0.856706, -0.493831, -0.148949;
8:   0.822228,  0.000000, -0.569158;
9:   0.550834,  0.425872, -0.717784 ;
10:   0.468173,  0.834308, -0.291108 ;
11:  0.515933,  0.808894,  0.281963 ;
12:  0.391890,  0.515855,  0.761785 ;
13:  0.478151,  0.000000,  0.878278 ;
14:  0.391890, -0.515855,  0.761785 ;
15:  0.515933, -0.808894,  0.281963 ;
16:  0.468173, -0.834308, -0.291108 ;
17:  0.550834, -0.425872, -0.717784 ;
18:  0.111012, -0.264029, -0.958105 ;
19:  0.111012,  0.264029, -0.958105 ;
20:  0.031984,  0.799591, -0.599693 ;

On Tue, Aug 7, 2012 at 10:43 AM, Judy James <jjames2 at umc.edu> wrote:

>  Dear members,
> I have a question about a data set I received from Siemens Verio.
> The images are in Mosaic form with 63 sets of 28 images in it. The DICOM
> header says 20 directions with 1 average. I don't understand how it has 63
> sets of mosaic if it was only 20 directions.
>
> Can any one help?
> I am also on the look out for the 20 direction gradient table used on
> Verio. Can any one share it?
>
> Thanks
> Judy
>
>
>
> Individuals who have received this information in error or are not
> authorized to receive it must promptly return or dispose of the information
> and notify the sender. Those individuals are hereby notified that they are
> strictly prohibited from reviewing, forwarding, printing, copying,
> distributing or using this information in any way.
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From junjie at dom.wustl.edu  Thu Aug 16 14:10:18 2012
From: junjie at dom.wustl.edu (Chen, Junjie)
Date: Thu, 16 Aug 2012 13:10:18 -0500
Subject: [Mristudio-users] Question: what is the user defined datatype
 "SLICE_ORI" and "SLICE_SEQ" , in fiberdata file header
Message-ID: <21C3B9BA004F9F458C8A07C4021C691CCF69BE19@DOMMAIL01.DOM.wustl.edu>

Dear MRI Studio:

  I'm asking for your help about the structure of the DtiStudio format for tracked fibers.

  I want extract fiber coordinates data using Matlab.  While I'm following the sample C code in FAQ (https://www.mristudio.org/wiki/faq ), it's unclear what the "SLICE_ORI" and "SLICE_SEQ" data type  are.     I will greatly appreciate your help on this.

  Regards


Junjie Chen, Sc.D.
Research Instructor
Washington University School of Medicine
St. Louis, MO, USA

Tel: 314-454-7411
Fax: 314-454-7490





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From lujiaoluo1990 at 126.com  Mon Aug 20 07:02:11 2012
From: lujiaoluo1990 at 126.com (=?GBK?B?wt7otL2/?=)
Date: Mon, 20 Aug 2012 19:02:11 +0800 (CST)
Subject: [Mristudio-users] the use of dtistudio, roieditor, and diffeomap
In-Reply-To: <CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A380E44FD@e14mbx10n.Enterprise.emory.net>
	<CAEq9apLNf=fiji=BAiea-QT=YOLy56gKaTw2oQgV1C6zBXSioQ@mail.gmail.com>
Message-ID: <7971590.1f367.13943b2724c.Coremail.lujiaoluo1990@126.com>

 Hi, dtistudio experts,
 I downloaded and installed the dtistudio, roieditor, and diffeomap software on my computer, but I am really confused that which one to use first, since I found that both dtistudio and diffeomap can do automatic image registeration, and both the dtistudio and roieditor can calculate the FA?ADC,MD, and do statistics. So I am really wondering that what's the relationship between these three softwares. Which one is suitable for me to process the DTI data?
 
Another question, when drawing roi, how can I locate V1 or FFA (these two are our region of interest) on the image precisely? 
 
Looking forward for your reply and thanks so much for your help?

 
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From raviteja.kotikalapudi at gmail.com  Mon Aug 20 12:33:26 2012
From: raviteja.kotikalapudi at gmail.com (Kotikalapudi Raviteja)
Date: Mon, 20 Aug 2012 17:33:26 +0100
Subject: [Mristudio-users] DTI images from VErio
In-Reply-To: <CAEq9apJ8Yc9S5jRA=0854Z1Q=wFhP7RPX8oOPTo3H31=J8ux1A@mail.gmail.com>
References: <F9DA9BCC8A26774E918E48363019D45551ED43D2@NTExMbx7.ntummc.umsmed.edu>
	<CAEq9apJ8Yc9S5jRA=0854Z1Q=wFhP7RPX8oOPTo3H31=J8ux1A@mail.gmail.com>
Message-ID: <CAGJ50wbahbBrntf124zXFEjhETZDhgCXCAvv-bKYGGFebFjuTg@mail.gmail.com>

Dear Susumu,

I am writing this mail in context with the image orientation problems
encountered while registering DTI to T2.

I would like to know if there is a way to solve this one, as I need to
normalize them further to a template image.

Thank you,
---KRT

On Thu, Aug 16, 2012 at 11:22 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Judy,
>
> I guess you did 3 signal averaging?
> In Siemens scanners, the signal averaging doesn't really average the data
> and save all scans in separate files. So, you may have 3 repetitions of
> 1+20.
>
> For the table, please try this;
>
> 0:   0, 0, 0
> 1:   1.000000,  0.000000,  0.000000;
> 2:   0.000000,  1.000000,  0.000000;
> 3:  -0.031984,  0.799591,  0.599693;
> 4:   0.856706,  0.493831, -0.148949;
> 5:   0.834429,  0.309159,  0.456234;
> 6:   0.834429, -0.309159,  0.456234;
> 7:   0.856706, -0.493831, -0.148949;
> 8:   0.822228,  0.000000, -0.569158;
> 9:   0.550834,  0.425872, -0.717784 ;
> 10:   0.468173,  0.834308, -0.291108 ;
> 11:  0.515933,  0.808894,  0.281963 ;
> 12:  0.391890,  0.515855,  0.761785 ;
> 13:  0.478151,  0.000000,  0.878278 ;
> 14:  0.391890, -0.515855,  0.761785 ;
> 15:  0.515933, -0.808894,  0.281963 ;
> 16:  0.468173, -0.834308, -0.291108 ;
> 17:  0.550834, -0.425872, -0.717784 ;
> 18:  0.111012, -0.264029, -0.958105 ;
> 19:  0.111012,  0.264029, -0.958105 ;
> 20:  0.031984,  0.799591, -0.599693 ;
>
> On Tue, Aug 7, 2012 at 10:43 AM, Judy James <jjames2 at umc.edu> wrote:
>
>>  Dear members,
>> I have a question about a data set I received from Siemens Verio.
>> The images are in Mosaic form with 63 sets of 28 images in it. The DICOM
>> header says 20 directions with 1 average. I don't understand how it has 63
>> sets of mosaic if it was only 20 directions.
>>
>> Can any one help?
>> I am also on the look out for the 20 direction gradient table used on
>> Verio. Can any one share it?
>>
>> Thanks
>> Judy
>>
>>
>>
>> Individuals who have received this information in error or are not
>> authorized to receive it must promptly return or dispose of the information
>> and notify the sender. Those individuals are hereby notified that they are
>> strictly prohibited from reviewing, forwarding, printing, copying,
>> distributing or using this information in any way.
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From m.tazeroualti at medtechsurgical.com  Tue Aug 21 05:13:03 2012
From: m.tazeroualti at medtechsurgical.com (Mohammed Tazeroualti)
Date: Tue, 21 Aug 2012 11:13:03 +0200
Subject: [Mristudio-users]  DTI PHILIPS Achieva
Message-ID: <93B3C308CBF36F40B9D21D91D2C95ADD38043EFE5C@MTSRVSBS.medtech.local>

I'm very (very) beginner in the manipulation of medical imageries.
I talk to you as specialists about the DTI issue.
Thank you in advance for your patience and help.

I has a sequence taken with a DTI PHILIPS Achieva composed of a DICOMDIR and a list of files:
- 1541 DICOM files: IM0001 to IM1541
- 2 files: XX_0181 and XX_1542
After analyzing the DICOM header:
- IM0001 to IM0180 files and XX0181 are standard MRI slices.
- IM0182 to IM1541 files and XX1542 are DWI slices.
- DWI slices are grouped by package 17 with the following values:
FILE|InstanceNumber|BValue|GradientOrientation
CD4 3D&DTI\DICOM\IM_0182|16|0|
CD4 3D&DTI\DICOM\IM_0183|17|800|-0.50, -0.50, -0.71
CD4 3D&DTI\DICOM\IM_0184|18|800|-0.50, -0.50, 0.71
CD4 3D&DTI\DICOM\IM_0185|19|800|0.71, -0.71, -0.00
CD4 3D&DTI\DICOM\IM_0186|20|800|-0.11, -0.71, -0.70
CD4 3D&DTI\DICOM\IM_0187|21|800|0.29, -0.70, -0.65
CD4 3D&DTI\DICOM\IM_0188|22|800|0.63, -0.33, -0.70
CD4 3D&DTI\DICOM\IM_0189|23|800|0.66, -0.27, -0.70
CD4 3D&DTI\DICOM\IM_0190|24|800|-0.67, -0.54, -0.50
CD4 3D&DTI\DICOM\IM_0191|25|800|0.70, -0.49, 0.51
CD4 3D&DTI\DICOM\IM_0192|26|800|-0.69, -0.25, 0.68
CD4 3D&DTI\DICOM\IM_0193|27|800|-0.71, -0.71, 0.03
CD4 3D&DTI\DICOM\IM_0194|28|800|-0.28, -0.71, 0.65
CD4 3D&DTI\DICOM\IM_0195|29|800|0.29, -0.70, 0.65
CD4 3D&DTI\DICOM\IM_0196|30|800|0.71, -0.71, 0.05
CD4 3D&DTI\DICOM\IM_0197|31|800|0.70, -0.20, 0.68
CD4 3D&DTI\DICOM\IM_0198|32|800|


My questions are:
1 - Why two files are named XX0181 and XX1542 instead of IM0181 and IM1542 and what did they in particular.
2 - DWI is grouped by package 17 it is the number of gradient? And is this number stored in a DICOM field?
3 - The image 0182 has a bValue equal to 0: Is it also a conventional MRI?
4 - The image 0198 has a bValue equal to 800 and no gradient, why?
5 - What are the other interesting DICOM fields for the treatment of DTI imaging?

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From kbekaath at yahoo.gr  Wed Sep 12 10:07:18 2012
From: kbekaath at yahoo.gr (=?UTF-8?B?zprOsc+EzrXPgc6vzr3OsSDOnM+Azq3Ous6x?=)
Date: Wed, 12 Sep 2012 14:07:18 +0000 (UTC)
Subject: [Mristudio-users] Invitation to connect on LinkedIn
Message-ID: <445307329.738033.1347458838879.JavaMail.app@ela4-app2318.prod>

LinkedIn
------------



ROI Editor, DiffeoMa,

I'd like to add you to my professional network on LinkedIn.

- ????????

???????? ?????
radiologist at BIOCOLLOIDS FATE AND TRANSPORT IN ENVIRONMENTAL SYSTEMS, NETWORK BIOMET
Greece

Confirm that you know ???????? ?????:
https://www.linkedin.com/e/-d2p9nf-h70i7a6w-4b/isd/8616772487/-I-AmMQy/?hs=false&tok=1AUXXeK7kLHlo1

--
You are receiving Invitation to Connect emails. Click to unsubscribe:
http://www.linkedin.com/e/-d2p9nf-h70i7a6w-4b/l9ys6G0wJq1XvKOY-vsMhGuLEHp2dn9j9rKxhG_fS613/goo/mristudio-users%40mristudio%2Eorg/20061/I2898267521_1/?hs=false&tok=3qSzBaO_ELHlo1

(c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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From rumamadhu at yahoo.com  Sat Sep 15 14:18:24 2012
From: rumamadhu at yahoo.com (Ruma Madhu)
Date: Sat, 15 Sep 2012 11:18:24 -0700 (PDT)
Subject: [Mristudio-users] (no subject)
Message-ID: <1347733104.75221.YahooMailClassic@web111601.mail.gq1.yahoo.com>

Hai,

I am presently working with DTI Studio and i find it difficult to draw optic radiations with it, Coud you please tell me
1. where to put ROI for optic radiation 
2.How can you get fine `thread like ` tracts with DTI-

Regards R? Sreedharan
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From susumu at mri.jhu.edu  Sat Sep 15 18:14:28 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 15 Sep 2012 18:14:28 -0400
Subject: [Mristudio-users] (no subject)
In-Reply-To: <1347733104.75221.YahooMailClassic@web111601.mail.gq1.yahoo.com>
References: <1347733104.75221.YahooMailClassic@web111601.mail.gq1.yahoo.com>
Message-ID: <CAEq9apJhQCakP9515JqCiE2_KMj_2khLNjz6cWb=5wdgxfF-wg@mail.gmail.com>

The optic radiation has a very sharp turn after it exits the LGN and is
difficult to reconstruct reliably with the 2-2.5mm resolution of regular
DTI.

Unfortunately, we can't control the thickness of the streamlines in
DtiStudio.

On Sat, Sep 15, 2012 at 2:18 PM, Ruma Madhu <rumamadhu at yahoo.com> wrote:

> Hai,
>
> I am presently working with DTI Studio and i find it difficult to draw
> optic radiations with it, Coud you please tell me
> 1. where to put ROI for optic radiation
> 2.How can you get fine `thread like ` tracts with DTI-
>
> Regards R  Sreedharan
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From Uzeyir.Ahmadli at usz.ch  Tue Sep 18 05:37:25 2012
From: Uzeyir.Ahmadli at usz.ch (Ahmadli Uzeyir)
Date: Tue, 18 Sep 2012 09:37:25 +0000
Subject: [Mristudio-users] (no subject)
In-Reply-To: <1347733104.75221.YahooMailClassic@web111601.mail.gq1.yahoo.com>
References: <1347733104.75221.YahooMailClassic@web111601.mail.gq1.yahoo.com>
Message-ID: <5C1876F4495A834CAE74C35EE218C38E4EFED597@DS-00520.usz.ch>

Hi Ruma,



you can easly reconstruct optic radiation using also "retrograde" tracking.

put your rois in occipital lobe and then cut away the fibers that do not enter LGN.



regards

Uzeyir

________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Ruma Madhu [rumamadhu at yahoo.com]
Sent: Saturday, September 15, 2012 20:18
To: mristudio-users at mristudio.org
Cc: Ruma M Sreedharan
Subject: [Mristudio-users] (no subject)

Hai,

I am presently working with DTI Studio and i find it difficult to draw optic radiations with it, Coud you please tell me
1. where to put ROI for optic radiation
2.How can you get fine `thread like ` tracts with DTI-

Regards R  Sreedharan


From lightgiving2004 at gmail.com  Tue Sep 18 23:17:07 2012
From: lightgiving2004 at gmail.com (Luke Back)
Date: Wed, 19 Sep 2012 12:17:07 +0900
Subject: [Mristudio-users] Questions on the Functions of DTI Studio
In-Reply-To: <DD7AC5C501BF624E8FA2BC897D4FA74C07A0A7EA@RAD-EXCH-SRV14.win.ad.jhu.edu>
References: <CAH0q4O+L13mkuuBrvbb=V7mzPJVuB-A=evcY0fh4+0Nmrq5hvQ@mail.gmail.com>
	<DD7AC5C501BF624E8FA2BC897D4FA74C07A0A590@RAD-EXCH-SRV14.win.ad.jhu.edu>
	<CAH0q4O+WnW0g_sLFA=K+hb+Kj=cv1x2fW=7HZ6ri8UrWKNnEaw@mail.gmail.com>
	<DD7AC5C501BF624E8FA2BC897D4FA74C07A0A7EA@RAD-EXCH-SRV14.win.ad.jhu.edu>
Message-ID: <CAH0q4O+yB_FspG6_fjbbhdJo3OdwhgX8QW2x8GCYguShEGJPiA@mail.gmail.com>

Dear Prof. Hangyi Jiang

I deeply appreciate your dedicated answers for my rough questions. To be
honest, I somewhat understand your comments and paper. To comprehend your
paper,I come to realize that I need to study and review again various
backgrounds including linear algebra, vectors, NMR spectroscopy, fluid
mechanics, and so on. Although it is not easy for me to understand your
thesis paper fully, I will step by step build up my knowlege to comprehend
it. I believe that your paper is worthy of my study analyzing my data.

Dear Prof. Jiang, however, I also need the best settings to analyze my data
practically. I am very concernd about my request that I would like you to
set up the optimal settings applied to my MRI pictures since this request
seems to be ill-mannered as a scholar. Yet I am just a graduate student
who needs to learn a lot of things. To understand your paper, I attempt to
teach myself linear algebra, vectors, NMR spectroscpy, fulid mechanics, and
so on, but I conclude that I require more time studying these things.

This is the reason I sent  all my data to you. I wish I could meet you
person to person and learn from you, but I could not. So could you please
help me to find out best settings for my case?I would like you to see my
case and give me the information of the optimal settings. Hopefully,I might
want you not to get offended by my petition.

I would like to be an expert for DTI studio someday, and your help will be
the starting point.

Thank you.
Sincerely Luke.



 TueI , Sep 18, 2012 at 12:05 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:

> hello,
>
>
>
> Q1: I do not understand why I choose to ?Create a mask?tab? and ?the
> number should be 150."
>
> I do not understand this function either
>
>
> A: we are not interesting in the "tensor" in the background area, the
> "background noise level" threshold will mask out the background area of the
> image. only the area within the brain will be calculated.  you can decide
> this threshold by read out the image intensities in the background area
> (usually do this based on the B0 image).  or you can create a "binary mask
> image" based on an anatomy image. in this "binary mask", the background
> area or the area you are not interested in are given a value 0,  all others
> are given a non-zero values. the program can use this "binary mask" to do
> same thing as the "background noise level" threshold does.
>
> Q2: I do not understand functions in Method tab and in Verify the result
> tab.
> Should I check or change any of these to obtain the optimal resolution?
>
> A: "verify the result" is usually used for automatic outlier rejection
> method. for your case, you may not need them.
>
>
> Q3: I do not understand why I put? the number,150,"  in the Background
> noise level tap
>
> A: see the answer for Q1;
>
> Q4: I do not understand why I uncheck ?Consider B-Value.?  I do not
> understand this function either
>
> A:  mathematically, B-value serves as a scaling factor for the results, if
> you are only interesting in the relative measurements (like FA map), don't
> worry about B-value. if you are interesting in absolute value of some
> measurement (like eigen values), B-value will scale down the read-out image
> intensities.  for detail, you may refer to the paper:
> Hangyi Jiang, Peter C.M. van Zijl, Jinsuh Kim, Godfrey D. Pearlson &
> Susumu Mori, "DtiStudio: Resource Program for Diffusion Tensor Computation
> and Fiber Bundle Tracking" Computer Methods and Programs in Biomedicine,
> vol. 81, pp106-116, 2006.
>
>
>
> : I do not understand why I put? the number,0.2,"  in the Start Tracking
> tap
>
>        I do not understand why I put? the number,0.2," and ?the number,
> 60,?respectively  in the Stop  Tracking tap.
>
>        I do not understand these functions either
>
>
> A:  these values control how will you do fiber tracking (when to start,
> when to stop..), again, you can refer the paper I mentioned above.
>
> best,
>
> hangyi
>
>
> ________________________________
> From: Luke Back [lightgiving2004 at gmail.com]
> Sent: Monday, September 17, 2012 4:59 AM
> To: Hangyi Jiang; mristudio-users at mristudio.org
> Subject: Re: Questions on the Functions of DTI Studio
>
> Dear Prof, Hangyi Jiang and DTI experts
> I am very grateful to your keen interests in my case and thoughtful
> answers. It was very helpful to my problems.
> Actually, I have another question on DTI settings.
> For this, I am attaching several documents including 1) DICOM file that I
> have studies, 2) a gradient table applied to DICOM files, and 3) DTI
> settings to which I apply.
> I would like you to help to find out the settings of the optimal
> resolution for my case so I could see the the clearest pictures derived
> from MRI.
> A friend of mine (she) taught me several numbers and conditions applied to
> my case, but she and I do not know anout each meaning of the number and
> condition as to why these numbers and conditions should be inserted into.
> She said that she also barely comprehended when learning.
> I ask five questions in the "DTI Data Analysis (The Basic Settings)"
> document I am attaching
> Could you please help me out for this matter?
>
> Thank you so much.
> Sincerely Luke.
>
> On Wed, Sep 12, 2012 at 3:32 AM, Hangyi Jiang <hjiang at jhmi.edu<mailto:
> hjiang at jhmi.edu>> wrote:
> hello, Luke,
>
> I got your questions from forwarded message.
>
> the ROI tools in "fiber" tab is used for fiber selection, only select
> fibers will be displayed,  but not the ROIs
> the ROI tools in "ROI" tab is used for simple ROI creation, not for fiber
> selection.
>
> if you just need one ROI for fiber selection (suppose that you used "OR"
> operation), you may use "ROI save" button (of the "ROI operations" group of
> the "fiber" tab) same the ROI as a binary image, and load the save image
> file in (file_format = RAW, data_type = BYTE), and take a look about ROI.
>
> if you used multiple ROIs for for fiber selection (e.g. using OR-AND
> combination), the situation is very complicated. you may need to save them
> as "binary map" to get a series binary images for each of ROIs.
>
> about your 2nd question, you may use "# of voxels of fiber passing
> through" as the measurement of you wanted.
>
> best,
>
> hangyi
>
>
> ________________________________
> From: Luke Back [lightgiving2004 at gmail.com<mailto:
> lightgiving2004 at gmail.com>]
> Sent: Monday, September 10, 2012 11:24 PM
> To: Xin Li; mristudio-users at mristudio.org<mailto:
> mristudio-users at mristudio.org>
> Subject: Questions on the Functions of DTI Studio
>
> Hello, DTIstudio Experts
>
> I am using this program so as to obtain FA, RA, radial and axial
> diffusivities. To do so, I am using ?ROI Drawing? function, attaining these
> parameters. Before that, I also primarily check my ROI (region of my
> interest) through ?Fiber Tracking? function to determine which parts I am
> supposed to draw. It is because that the fiber tracking section also
> includes ?ROI-Drawing Enable? function by which I could exactly see the
> anatomical parts I desire. For example, if my ROI is corpus callosum, I
> could see this part through the fiber tracking section.
>
> However, when I return to ?ROI? section, I no more use this information. I
> mean I should turn off ?ROI-Drawing Enable? function in ?Fiber Tracking?
> section. I re-draw the target. Due to this process, I do not know where the
> fibers I desire pass through because ?ROI Drawing-Operation?in ?ROI?
> section does not support fiber tracking information. Could you guys please
> solve this matter?
>
> One more question is that I am wondering if I calculate fiber volume after
> I draw ROI by ?ROI-Drawing Enable? function in ?Fiber Tracking? section.
>
> Overall, I summarize my questions as follows:
> 1)     How can I sustain ROI drawing in ?Fiber Tracking? section although
> I work in ?ROI? section?
> 2)     Is there way to calculate fiber volume after I draw ROI by
> ?ROI-Drawing Enable? function in ?Fiber Tracking? section?
> p.s. I am attaching what I have done
>
>
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From delfyettwt at upmc.edu  Wed Sep 19 10:32:09 2012
From: delfyettwt at upmc.edu (Delfyett, William T)
Date: Wed, 19 Sep 2012 14:32:09 +0000
Subject: [Mristudio-users] Available open source normal dti data sets?
Message-ID: <28B58DD6A1D6124CAA38E450B92898F812A7CF3B@MSXMBXNSPRD11.acct.upmchs.net>

Hello, 

Could anyone suggest or point me to any available normal dti data sets specifically for adolescent patients/subjects?  I have not been able to find any substantial control data sets for subjects between 10 and 18 yrs of age or within that range.  Any suggestions would be greatly appreciated.

Thanks, 


Bill Delfyett

From susumu at mri.jhu.edu  Wed Sep 19 11:19:42 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Wed, 19 Sep 2012 11:19:42 -0400
Subject: [Mristudio-users] Available open source normal dti data sets?
In-Reply-To: <28B58DD6A1D6124CAA38E450B92898F812A7CF3B@MSXMBXNSPRD11.acct.upmchs.net>
References: <28B58DD6A1D6124CAA38E450B92898F812A7CF3B@MSXMBXNSPRD11.acct.upmchs.net>
Message-ID: <CAEq9apKjFrJJkeqdseOYE0x5a-KxnwafvNEYU71kzF0fhnkfrQ@mail.gmail.com>

We have some pediatric database in lbam.med.jhmi.edu.
You can download the data from there.

On Wed, Sep 19, 2012 at 10:32 AM, Delfyett, William T
<delfyettwt at upmc.edu>wrote:

> Hello,
>
> Could anyone suggest or point me to any available normal dti data sets
> specifically for adolescent patients/subjects?  I have not been able to
> find any substantial control data sets for subjects between 10 and 18 yrs
> of age or within that range.  Any suggestions would be greatly appreciated.
>
> Thanks,
>
>
> Bill Delfyett
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From cyrus at vtc.vt.edu  Mon Oct  1 14:33:27 2012
From: cyrus at vtc.vt.edu (Cyrus Eierud)
Date: Mon, 01 Oct 2012 18:33:27 +0000
Subject: [Mristudio-users] Reference for JHU_GA DTI map
Message-ID: <DBF07F512FBA894E8B902EDBF9A3DB2F08FC5F33@gellar.vtcri.local>

Dear DtiStudio Editor,

In accordance to earlier post (Mon, Apr 9, 2012 at 9:27 PM, Rachael Gonzales) I noticed that DtiStudio should be referenced by Comput Methods Programs Biomed 2006;81(2):106-116, PMC. If I just want to reference the JHU_GA map, should I then use the same reference?

Thanks in Advance,
Cyrus Eierud


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From susumu at mri.jhu.edu  Mon Oct  1 15:59:18 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 01 Oct 2012 15:59:18 -0400
Subject: [Mristudio-users] Reference for JHU_GA DTI map
In-Reply-To: <DBF07F512FBA894E8B902EDBF9A3DB2F08FC5F33@gellar.vtcri.local>
References: <DBF07F512FBA894E8B902EDBF9A3DB2F08FC5F33@gellar.vtcri.local>
Message-ID: <CAEq9apLJ+7E8useMGPWpF=t4Lpw-VzG7DGb+q7Y5MxctM9R+_g@mail.gmail.com>

Hi Cyrus,

Thank you for asking this question.
For the group-averaged atlas, please refer;

Mori S, Oishi K, Jiang H, Jiang L, Li X, Akhter K, Hua K, Faria AV, Mahmood
A, Woods R, Toga AW, Pike GB, Neto PR, Evans A, Zhang J, Huang H, Miller
MI, van Zijl P, Mazziotta J. Stereotaxic white matter atlas based on
diffusion tensor imaging in an ICBM template. Neuroimage
2008;40(2):570-582, PMC2478641

Thanks,

Susumu

On Mon, Oct 1, 2012 at 2:33 PM, Cyrus Eierud <cyrus at vtc.vt.edu> wrote:

>  Dear DtiStudio Editor,
>
>  In accordance to earlier post (Mon, Apr 9, 2012 at 9:27 PM, Rachael
> Gonzales) I noticed that DtiStudio should be referenced by Comput Methods
> Programs Biomed 2006;81(2):106-116, PMC. If I just want to reference the
> JHU_GA map, should I then use the same reference?
>
>  Thanks in Advance,
> Cyrus Eierud
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From cyrus at vtc.vt.edu  Mon Oct  1 16:11:46 2012
From: cyrus at vtc.vt.edu (Cyrus Eierud)
Date: Mon, 01 Oct 2012 20:11:46 +0000
Subject: [Mristudio-users] Reference for JHU_GA DTI map
In-Reply-To: <CAEq9apLJ+7E8useMGPWpF=t4Lpw-VzG7DGb+q7Y5MxctM9R+_g@mail.gmail.com>
Message-ID: <DBF07F512FBA894E8B902EDBF9A3DB2F08FC5FCA@gellar.vtcri.local>

Thank You!

Best Regards,
Cyrus Eierud
Graduate student in the LaConte Lab
Virginia Tech Carilion Research Institute
Mobile (540) 314-6449

From: susumu mori <susumu at mri.jhu.edu<mailto:susumu at mri.jhu.edu>>
Reply-To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>>
Date: Mon, 1 Oct 2012 15:59:18 -0400
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>>
Subject: Re: [Mristudio-users] Reference for JHU_GA DTI map

Hi Cyrus,

Thank you for asking this question.
For the group-averaged atlas, please refer;

Mori S, Oishi K, Jiang H, Jiang L, Li X, Akhter K, Hua K, Faria AV, Mahmood A, Woods R, Toga AW, Pike GB, Neto PR, Evans A, Zhang J, Huang H, Miller MI, van Zijl P, Mazziotta J. Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template. Neuroimage 2008;40(2):570-582, PMC2478641

Thanks,

Susumu

On Mon, Oct 1, 2012 at 2:33 PM, Cyrus Eierud <cyrus at vtc.vt.edu<mailto:cyrus at vtc.vt.edu>> wrote:
Dear DtiStudio Editor,

In accordance to earlier post (Mon, Apr 9, 2012 at 9:27 PM, Rachael Gonzales) I noticed that DtiStudio should be referenced by Comput Methods Programs Biomed 2006;81(2):106-116, PMC. If I just want to reference the JHU_GA map, should I then use the same reference?

Thanks in Advance,
Cyrus Eierud



_______________________________________________
mristudio-users mailing list
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http://lists.mristudio.org/mailman/listinfo/
Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>


_______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org> http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<mailto:mristudio-users-unsubscribe at mristudio.org>
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From hkim at peds.uab.edu  Tue Oct  2 11:41:39 2012
From: hkim at peds.uab.edu (Hyunmi Kim, M.D.)
Date: Tue, 02 Oct 2012 15:41:39 +0000
Subject: [Mristudio-users] Phillips Ingenia 3T-DTI Tensor file
In-Reply-To: <AANLkTinTQSk1xB8ujamNETKocUhz6-3ewqYyQkRv8gpB@mail.gmail.com>
References: <AANLkTimFuwiJUYLJfkxEgQNzx2Wmz-qtvuJB+RYAYYuC@mail.gmail.com>
	<AANLkTinTQSk1xB8ujamNETKocUhz6-3ewqYyQkRv8gpB@mail.gmail.com>
Message-ID: <F4859B6CB08E3C40B5A65AF9DB91C17D18AD2AB7@EXDB3-PEDS.peds.uab.edu>

Dear supporter;

I would like to have a Phillips Ingenia 3T-DTI Tensor file.
Is it available to you?
Thank you for your help.


Hyunmi Kim, MD, PhD, MPH

Associate Professor

Division of Pediatric Neurology

University Alabama at Birmingham

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From jie.jiang at emory.edu  Mon Nov 19 13:22:04 2012
From: jie.jiang at emory.edu (Jiang, Jie)
Date: Mon, 19 Nov 2012 18:22:04 +0000
Subject: [Mristudio-users] how to calculate MD
Message-ID: <EE3B3A5800B7A946926FDDC1DBAD5C2A4407BE1F@e14mbx12n.Enterprise.emory.net>

  Hi, dtistudio experts,
I used the DTIstudio to calculate the FA map and it works well. But I cannot find the way to calculate the MD in my version (3.0.3)? Any suggestion? Thank you.
jie

________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
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From susumu at mri.jhu.edu  Mon Nov 19 14:25:50 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 19 Nov 2012 14:25:50 -0500
Subject: [Mristudio-users] how to calculate MD
In-Reply-To: <EE3B3A5800B7A946926FDDC1DBAD5C2A4407BE1F@e14mbx12n.Enterprise.emory.net>
References: <EE3B3A5800B7A946926FDDC1DBAD5C2A4407BE1F@e14mbx12n.Enterprise.emory.net>
Message-ID: <CAEq9apKOKh-48TjU=5RJeL3rKTAcxbS4GQ9tONQDWAQx7tHLMQ@mail.gmail.com>

In DtiStudio, we use a term called "Trace".
If you divide this by 3, you get "Mean Diffusivity".

On Mon, Nov 19, 2012 at 1:22 PM, Jiang, Jie <jie.jiang at emory.edu> wrote:

>    Hi, dtistudio experts,
> I used the DTIstudio to calculate the FA map and it works well. But I
> cannot find the way to calculate the MD in my version (3.0.3)? Any
> suggestion? Thank you.
> jie
>
> ------------------------------
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From 731961630 at qq.com  Tue Nov 20 05:37:20 2012
From: 731961630 at qq.com (=?utf-8?B?6LW15pWP?=)
Date: Tue, 20 Nov 2012 18:37:20 +0800
Subject: [Mristudio-users] =?utf-8?b?5Zue5aSN77yaICBob3cgdG8gY2FsY3VsYXRl?=
 =?utf-8?q?_MD?=
Message-ID: <tencent_064E7FA825C305D602178A9B@qq.com>

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From 731961630 at qq.com  Tue Nov 20 05:39:38 2012
From: 731961630 at qq.com (=?utf-8?B?6LW15pWP?=)
Date: Tue, 20 Nov 2012 18:39:38 +0800
Subject: [Mristudio-users] =?utf-8?b?5Zue5aSN77yaICBob3cgdG8gY2FsY3VsYXRl?=
 =?utf-8?q?_MD?=
Message-ID: <tencent_2D2ACEB86286F8483420EBDC@qq.com>

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From jie.jiang at emory.edu  Tue Nov 20 09:45:52 2012
From: jie.jiang at emory.edu (Jiang, Jie)
Date: Tue, 20 Nov 2012 14:45:52 +0000
Subject: [Mristudio-users] =?gb2312?b?IFJFOiAgu9i4tKO6ICBob3cgdG8gY2FsY3Vs?=
 =?gb2312?b?YXRlIE1E?=
In-Reply-To: <tencent_2D2ACEB86286F8483420EBDC@qq.com>
References: <tencent_2D2ACEB86286F8483420EBDC@qq.com>
Message-ID: <EE3B3A5800B7A946926FDDC1DBAD5C2A4407BEA0@e14mbx12n.Enterprise.emory.net>

I got it. Thank you all for your help.
Best,
Jie
________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of ?? [731961630 at qq.com]
Sent: Tuesday, November 20, 2012 5:39 AM
To: DTI Studio, ROI Editor,DiffeoM
Subject: [Mristudio-users] ??? how to calculate MD

Hi,Jie,
I have read your email seriously,though I really want to help you,I am not able to give you some practical suggestions for my level ,you can ask somebody else,good luck to you!
Amy

------------------
Best regards,

Amin Ma
-----------------------------------------------
School of Bioscience and Bioengineering
South China University of Technology
Guangzhou, China 510006
Phone:13763355576
QQ:731961630
E-mail: 731961630 at qq.com<mailto:731961630 at qq.com>



------------------ ???? ------------------
???: "susumu mori"<susumu at mri.jhu.edu>;
????: 2012?11?20?(???) ??3:25
???: "DTI Studio, ROI Editor, DiffeoMap Questions/Support"<mristudio-users at mristudio.org>;
??: Re: [Mristudio-users] how to calculate MD

In DtiStudio, we use a term called "Trace".
If you divide this by 3, you get "Mean Diffusivity".

On Mon, Nov 19, 2012 at 1:22 PM, Jiang, Jie <jie.jiang at emory.edu<mailto:jie.jiang at emory.edu>> wrote:
  Hi, dtistudio experts,
I used the DTIstudio to calculate the FA map and it works well. But I cannot find the way to calculate the MD in my version (3.0.3)? Any suggestion? Thank you.
jie

________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).

_______________________________________________
mristudio-users mailing list
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http://lists.mristudio.org/mailman/listinfo/
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From santoshyadav20076 at gmail.com  Mon Nov 26 01:28:36 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Mon, 26 Nov 2012 11:58:36 +0530
Subject: [Mristudio-users] Slice thickness of DTI
Message-ID: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>

Hi DTI experts,

Thanks for great supports!

I would like know the recommended slice thickness and gap between the slice
for DTI data acquisition for 12 directions. Is higher Slice thickness( more
that 3 mm) have partial volume effect?

Second question: Is eye open during the DTI acquisition have any impact on
DTI distortion or image quality?

With Best Regards,

Santosh
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From susumu at mri.jhu.edu  Mon Nov 26 07:31:55 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Mon, 26 Nov 2012 07:31:55 -0500
Subject: [Mristudio-users] Slice thickness of DTI
In-Reply-To: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>
References: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>
Message-ID: <CAEq9apJo8aBHqsxHwVh8KJ7TY8VOhY_Li-UJqGvxC_EetLH=tQ@mail.gmail.com>

Hi Santosh,

Practically, the slice thickness, which is the thinner the better, is
determined by SNR.
If you use 2.5 mm, you need about 50-55 slices to cover the entire brain.
2.2 mm needs 55-60 and 2mm needs more than 60. These are all without gaps.

With 5-6 min scans, you can acquire about 40-50 DWIs for 2.5mm/50-slice 3D
data. These numbers decrease as the thickness become thinner and thus more
slices are required and takes longer time.

40-50DWI means about 4 repetitions of 12-orientations.

If you use a 1.5T, you may need more than 60 DWIs with 2.5mm, which takes
about 7-8min. With thinner slices (e.g. 2.2mm), you need longer scans to
achieve good SNR.

With a 3T, 30-40 DWIs would give decent SNR with 2.5mm. With 2-2.2mm slice,
you want more than 50-60 DWIs (5-8min).

These numbers are to achieve a good SNR, which depends on my subjective
judgement. So different people could recommend different numbers, but they
may not be that much different.

As for image distortion, the most important factor is the size of the image
matrix; the smaller the better (I assume that you already use parallel
imaging, which reduces the matrix size into half).

For example, 128x128points / 256x256mm and 96x96/192x192mm both give the
same 2mm resolution, but 96x96 would give better (less) distortion and
better SNR.

On Mon, Nov 26, 2012 at 1:28 AM, Santosh Yadav
<santoshyadav20076 at gmail.com>wrote:

> Hi DTI experts,
>
> Thanks for great supports!
>
> I would like know the recommended slice thickness and gap between the
> slice for DTI data acquisition for 12 directions. Is higher
> Slice thickness( more that 3 mm) have partial volume effect?
>
> Second question: Is eye open during the DTI acquisition have any impact on
> DTI distortion or image quality?
>
> With Best Regards,
>
> Santosh
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From santoshyadav20076 at gmail.com  Mon Nov 26 15:56:32 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Mon, 26 Nov 2012 10:56:32 -1000
Subject: [Mristudio-users] Slice thickness of DTI
In-Reply-To: <CAEq9apJo8aBHqsxHwVh8KJ7TY8VOhY_Li-UJqGvxC_EetLH=tQ@mail.gmail.com>
References: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>
	<CAEq9apJo8aBHqsxHwVh8KJ7TY8VOhY_Li-UJqGvxC_EetLH=tQ@mail.gmail.com>
Message-ID: <CA+7fnM1o-NzJ5z_+=jT3QBYox69JfOLjKy4LkK4=c0e7H6=Qsw@mail.gmail.com>

 Thanks a lot Sir,


I have another question regarding DTI data; I have longitudinal DTI data of
3 time points. First time point have 4 averages second time point have 2
averages and third time point have 4 averages, can I combine these data
sets?

So finally the question is what the effect of averaging of DTI data, is it
going to the change the DTI matrix such as FA and Trace?


With best Regards,


On Mon, Nov 26, 2012 at 2:31 AM, susumu mori <susumu at mri.jhu.edu> wrote:

> Hi Santosh,
>
> Practically, the slice thickness, which is the thinner the better, is
> determined by SNR.
> If you use 2.5 mm, you need about 50-55 slices to cover the entire brain.
> 2.2 mm needs 55-60 and 2mm needs more than 60. These are all without gaps.
>
> With 5-6 min scans, you can acquire about 40-50 DWIs for 2.5mm/50-slice 3D
> data. These numbers decrease as the thickness become thinner and thus more
> slices are required and takes longer time.
>
> 40-50DWI means about 4 repetitions of 12-orientations.
>
> If you use a 1.5T, you may need more than 60 DWIs with 2.5mm, which takes
> about 7-8min. With thinner slices (e.g. 2.2mm), you need longer scans to
> achieve good SNR.
>
> With a 3T, 30-40 DWIs would give decent SNR with 2.5mm. With 2-2.2mm
> slice, you want more than 50-60 DWIs (5-8min).
>
> These numbers are to achieve a good SNR, which depends on my subjective
> judgement. So different people could recommend different numbers, but they
> may not be that much different.
>
> As for image distortion, the most important factor is the size of the
> image matrix; the smaller the better (I assume that you already use
> parallel imaging, which reduces the matrix size into half).
>
> For example, 128x128points / 256x256mm and 96x96/192x192mm both give the
> same 2mm resolution, but 96x96 would give better (less) distortion and
> better SNR.
>
> On Mon, Nov 26, 2012 at 1:28 AM, Santosh Yadav <
> santoshyadav20076 at gmail.com> wrote:
>
>> Hi DTI experts,
>>
>> Thanks for great supports!
>>
>> I would like know the recommended slice thickness and gap between the
>> slice for DTI data acquisition for 12 directions. Is higher
>> Slice thickness( more that 3 mm) have partial volume effect?
>>
>> Second question: Is eye open during the DTI acquisition have any impact
>> on DTI distortion or image quality?
>>
>> With Best Regards,
>>
>> Santosh
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>


-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From susumu at mri.jhu.edu  Tue Nov 27 09:07:36 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Tue, 27 Nov 2012 09:07:36 -0500
Subject: [Mristudio-users] Slice thickness of DTI
In-Reply-To: <CA+7fnM1o-NzJ5z_+=jT3QBYox69JfOLjKy4LkK4=c0e7H6=Qsw@mail.gmail.com>
References: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>
	<CAEq9apJo8aBHqsxHwVh8KJ7TY8VOhY_Li-UJqGvxC_EetLH=tQ@mail.gmail.com>
	<CA+7fnM1o-NzJ5z_+=jT3QBYox69JfOLjKy4LkK4=c0e7H6=Qsw@mail.gmail.com>
Message-ID: <CAEq9ap+HRn0fj08cyEk_f+xp035ChskbmR1Zp=nH5sQDu7=mew@mail.gmail.com>

When you consider effects of imaging parameters on the final outcomes, you
need to know variability and bias.
If the outcomes have simple Gaussian noises, less scans (thus lower SNR)
would lead to higher variability. In your case, suppose you draw an ROI on
the internal capsule and measure Trace of 100 voxels in the ROI, your
second time points would have larger standard deviations. However, you
could argue that the average values are still comparable.

FA is known to have bias; as SNR goes down (e.g. less signal averaging), FA
goes up. Depending on tensor fitting algorithm, completely random noise
seem to converge at around 0.8 - 1.0 or even higher. As SNR goes up, the
measured FA values converge to the real FA value.

If your image protocol have sufficient SNR with 1 signal averaging such
that the measured FA values are already close to the real FA values, then
you won't see much impact between 2 and 4 signal averaging. If your image
protocol has sufficient SNR with 4 averaging but not with 2 averaging, you
would see uniformly higher FA with 2 signal averaging. In this case, you
can't combine the data. Practically, if you are using 12-orientation / 3T /
2.5mm protocol, you may find FA increase with 2 averaging compared to 4. If
you are using protocols with less SNR (e.g. 2mm resolution or 1.5T), the
effect would be worse.

On Mon, Nov 26, 2012 at 3:56 PM, Santosh Yadav
<santoshyadav20076 at gmail.com>wrote:

>  Thanks a lot Sir,
>
>
> I have another question regarding DTI data; I have longitudinal DTI data
> of 3 time points. First time point have 4 averages second time point have 2
> averages and third time point have 4 averages, can I combine these data
> sets?
>
> So finally the question is what the effect of averaging of DTI data, is it
> going to the change the DTI matrix such as FA and Trace?
>
>
> With best Regards,
>
>
>
> On Mon, Nov 26, 2012 at 2:31 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Santosh,
>>
>> Practically, the slice thickness, which is the thinner the better, is
>> determined by SNR.
>> If you use 2.5 mm, you need about 50-55 slices to cover the entire brain.
>> 2.2 mm needs 55-60 and 2mm needs more than 60. These are all without gaps.
>>
>> With 5-6 min scans, you can acquire about 40-50 DWIs for 2.5mm/50-slice
>> 3D data. These numbers decrease as the thickness become thinner and thus
>> more slices are required and takes longer time.
>>
>> 40-50DWI means about 4 repetitions of 12-orientations.
>>
>> If you use a 1.5T, you may need more than 60 DWIs with 2.5mm, which takes
>> about 7-8min. With thinner slices (e.g. 2.2mm), you need longer scans to
>> achieve good SNR.
>>
>> With a 3T, 30-40 DWIs would give decent SNR with 2.5mm. With 2-2.2mm
>> slice, you want more than 50-60 DWIs (5-8min).
>>
>> These numbers are to achieve a good SNR, which depends on my subjective
>> judgement. So different people could recommend different numbers, but they
>> may not be that much different.
>>
>> As for image distortion, the most important factor is the size of the
>> image matrix; the smaller the better (I assume that you already use
>> parallel imaging, which reduces the matrix size into half).
>>
>> For example, 128x128points / 256x256mm and 96x96/192x192mm both give the
>> same 2mm resolution, but 96x96 would give better (less) distortion and
>> better SNR.
>>
>> On Mon, Nov 26, 2012 at 1:28 AM, Santosh Yadav <
>> santoshyadav20076 at gmail.com> wrote:
>>
>>> Hi DTI experts,
>>>
>>> Thanks for great supports!
>>>
>>> I would like know the recommended slice thickness and gap between the
>>> slice for DTI data acquisition for 12 directions. Is higher
>>> Slice thickness( more that 3 mm) have partial volume effect?
>>>
>>> Second question: Is eye open during the DTI acquisition have any impact
>>> on DTI distortion or image quality?
>>>
>>> With Best Regards,
>>>
>>> Santosh
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
>
> --
> With Best Regards,
>
> Neuroscience and MR Research Program
>
> Department of Medicine, Queen's Medical Center
>
> University of Hawaii
>
> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>
> Phone No. 808-220-7152
>
> Fax No.  808-545-8970
>
>
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From santoshyadav20076 at gmail.com  Wed Nov 28 03:24:28 2012
From: santoshyadav20076 at gmail.com (Santosh Yadav)
Date: Wed, 28 Nov 2012 13:54:28 +0530
Subject: [Mristudio-users] Slice thickness of DTI
In-Reply-To: <CAEq9ap+HRn0fj08cyEk_f+xp035ChskbmR1Zp=nH5sQDu7=mew@mail.gmail.com>
References: <CA+7fnM0BuXk5Uh8khXJ_2Cq++dNe3wprEqh7wTGbnwyLuz5BaA@mail.gmail.com>
	<CAEq9apJo8aBHqsxHwVh8KJ7TY8VOhY_Li-UJqGvxC_EetLH=tQ@mail.gmail.com>
	<CA+7fnM1o-NzJ5z_+=jT3QBYox69JfOLjKy4LkK4=c0e7H6=Qsw@mail.gmail.com>
	<CAEq9ap+HRn0fj08cyEk_f+xp035ChskbmR1Zp=nH5sQDu7=mew@mail.gmail.com>
Message-ID: <CA+7fnM0P2K5rr=B3=fz2mqiP5Cef4E6Mj1sXgqDD-T1+U3Dzhw@mail.gmail.com>

Dear Professor,

Thanks a lot for making a time and great supports.

With Best Regards

On Tue, Nov 27, 2012 at 7:37 PM, susumu mori <susumu at mri.jhu.edu> wrote:

> When you consider effects of imaging parameters on the final outcomes, you
> need to know variability and bias.
> If the outcomes have simple Gaussian noises, less scans (thus lower SNR)
> would lead to higher variability. In your case, suppose you draw an ROI on
> the internal capsule and measure Trace of 100 voxels in the ROI, your
> second time points would have larger standard deviations. However, you
> could argue that the average values are still comparable.
>
> FA is known to have bias; as SNR goes down (e.g. less signal averaging),
> FA goes up. Depending on tensor fitting algorithm, completely random noise
> seem to converge at around 0.8 - 1.0 or even higher. As SNR goes up, the
> measured FA values converge to the real FA value.
>
> If your image protocol have sufficient SNR with 1 signal averaging such
> that the measured FA values are already close to the real FA values, then
> you won't see much impact between 2 and 4 signal averaging. If your image
> protocol has sufficient SNR with 4 averaging but not with 2 averaging, you
> would see uniformly higher FA with 2 signal averaging. In this case, you
> can't combine the data. Practically, if you are using 12-orientation / 3T /
> 2.5mm protocol, you may find FA increase with 2 averaging compared to 4. If
> you are using protocols with less SNR (e.g. 2mm resolution or 1.5T), the
> effect would be worse.
>
>
> On Mon, Nov 26, 2012 at 3:56 PM, Santosh Yadav <
> santoshyadav20076 at gmail.com> wrote:
>
>>  Thanks a lot Sir,
>>
>>
>> I have another question regarding DTI data; I have longitudinal DTI data
>> of 3 time points. First time point have 4 averages second time point have 2
>> averages and third time point have 4 averages, can I combine these data
>> sets?
>>
>> So finally the question is what the effect of averaging of DTI data, is
>> it going to the change the DTI matrix such as FA and Trace?
>>
>>
>> With best Regards,
>>
>>
>>
>> On Mon, Nov 26, 2012 at 2:31 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>>
>>> Hi Santosh,
>>>
>>> Practically, the slice thickness, which is the thinner the better, is
>>> determined by SNR.
>>> If you use 2.5 mm, you need about 50-55 slices to cover the entire brain.
>>> 2.2 mm needs 55-60 and 2mm needs more than 60. These are all without
>>> gaps.
>>>
>>> With 5-6 min scans, you can acquire about 40-50 DWIs for 2.5mm/50-slice
>>> 3D data. These numbers decrease as the thickness become thinner and thus
>>> more slices are required and takes longer time.
>>>
>>> 40-50DWI means about 4 repetitions of 12-orientations.
>>>
>>> If you use a 1.5T, you may need more than 60 DWIs with 2.5mm, which
>>> takes about 7-8min. With thinner slices (e.g. 2.2mm), you need longer scans
>>> to achieve good SNR.
>>>
>>> With a 3T, 30-40 DWIs would give decent SNR with 2.5mm. With 2-2.2mm
>>> slice, you want more than 50-60 DWIs (5-8min).
>>>
>>> These numbers are to achieve a good SNR, which depends on my subjective
>>> judgement. So different people could recommend different numbers, but they
>>> may not be that much different.
>>>
>>> As for image distortion, the most important factor is the size of the
>>> image matrix; the smaller the better (I assume that you already use
>>> parallel imaging, which reduces the matrix size into half).
>>>
>>> For example, 128x128points / 256x256mm and 96x96/192x192mm both give the
>>> same 2mm resolution, but 96x96 would give better (less) distortion and
>>> better SNR.
>>>
>>> On Mon, Nov 26, 2012 at 1:28 AM, Santosh Yadav <
>>> santoshyadav20076 at gmail.com> wrote:
>>>
>>>> Hi DTI experts,
>>>>
>>>> Thanks for great supports!
>>>>
>>>> I would like know the recommended slice thickness and gap between the
>>>> slice for DTI data acquisition for 12 directions. Is higher
>>>> Slice thickness( more that 3 mm) have partial volume effect?
>>>>
>>>> Second question: Is eye open during the DTI acquisition have any impact
>>>> on DTI distortion or image quality?
>>>>
>>>> With Best Regards,
>>>>
>>>> Santosh
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing list
>>>> mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> mristudio-users-unsubscribe at mristudio.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>>
>> --
>> With Best Regards,
>>
>> Neuroscience and MR Research Program
>>
>> Department of Medicine, Queen's Medical Center
>>
>> University of Hawaii
>>
>> 1356 Lusitana Street, 7th Floor, Honolulu, HI 96813
>>
>> Phone No. 808-220-7152
>>
>> Fax No.  808-545-8970
>>
>>
>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>


-- 
With Best Regards,

Neuroscience and MR Research Program

Department of Medicine, Queen's Medical Center

University of Hawaii

1356 Lusitana Street, 7th Floor, Honolulu, HI 96813

Phone No. 808-220-7152

Fax No.  808-545-8970
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From alb.net at gmail.com  Wed Nov 28 11:48:00 2012
From: alb.net at gmail.com (Dorian P.)
Date: Wed, 28 Nov 2012 11:48:00 -0500
Subject: [Mristudio-users] ROI maps for DTIstudio
Message-ID: <CAF9pfmYZCaYyAz-G8FdHxfnuCuBangPvigdq_Mi0TR3jXvWb9w@mail.gmail.com>

Hi everybody and thank you for providing the MRIstudio course this week.

I have a problem with ROIs. My target is to create two ROIs with an "AND"
operation in fiber tracking (need to see fibers that pas from both). The
two ROIs will be taken from SPM.

What I did is create the first ROI and reslice it in SPM to the dimensions
of the colormap image. I imported the map in ROIeditor and it displays
correctly (byte image). Then I created a ROI based on thresholding values.
Saved the ROI as binary mask and expected to get the ".dat" and ".map"
files.

1. The binary maps produced by ROIeditor do not have a ".map" file. I find
only two ".dat" files. One of them is the map file and I can edit it in
Wordpad. I renamed this file to ".map" to open it in DTIstudio.

2. DTIstudio does not open the ".map" file anyway, it shows nothing on the
screen. However, when I open the raw ".dat" file the fibers are finally
shown. Still, this doesn't resolve my problem as I need two rois with an
AND operation.

3. I tried saving binary maps both from ROIeditor and DTIstudio but
DTIstudio can't open any of them. Beside, DTIstudio doesn't produce the
same files as ROIeditor. The extensions are different and rois from
DTIstudio have lines for the operation while rois from ROIeditor don't. I
tried adding those lines to the ".map" file of ROIeditor, without success.

Can you give me some hint how to perform my task.

Software versions:
Roieditor v1.5 - 64bit
DTIstudio v3.03 Sep 2010 - 64bit

Thank you.
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From xli16 at jhmi.edu  Wed Nov 28 13:21:20 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Wed, 28 Nov 2012 13:21:20 -0500
Subject: [Mristudio-users] ROI maps for DTIstudio
In-Reply-To: <CAF9pfmYZCaYyAz-G8FdHxfnuCuBangPvigdq_Mi0TR3jXvWb9w@mail.gmail.com>
References: <CAF9pfmYZCaYyAz-G8FdHxfnuCuBangPvigdq_Mi0TR3jXvWb9w@mail.gmail.com>
Message-ID: <71f094121f49f.50b60fd0@johnshopkins.edu>

Hi Dorian,

After you save your rois in ROIEditor as binary maps, please add lines for the operation, fiber color and color mode to the map file and try to load these binary map files into DtiStudio again.


Xin



----- Original Message -----
From: "Dorian P." <alb.net at gmail.com>
Date: Wednesday, November 28, 2012 11:48 am
Subject: [Mristudio-users] ROI maps for DTIstudio
To: mristudio-users at mristudio.org


> Hi everybody and thank you for providing the MRIstudio course this week.
>  
>  I have a problem with ROIs. My target is to create two ROIs with an "AND"
>  operation in fiber tracking (need to see fibers that pas from both). 
> The
>  two ROIs will be taken from SPM.
>  
>  What I did is create the first ROI and reslice it in SPM to the dimensions
>  of the colormap image. I imported the map in ROIeditor and it displays
>  correctly (byte image). Then I created a ROI based on thresholding values.
>  Saved the ROI as binary mask and expected to get the ".dat" and ".map"
>  files.
>  
>  1. The binary maps produced by ROIeditor do not have a ".map" file. I 
> find
>  only two ".dat" files. One of them is the map file and I can edit it 
> in
>  Wordpad. I renamed this file to ".map" to open it in DTIstudio.
>  
>  2. DTIstudio does not open the ".map" file anyway, it shows nothing 
> on the
>  screen. However, when I open the raw ".dat" file the fibers are finally
>  shown. Still, this doesn't resolve my problem as I need two rois with 
> an
>  AND operation.
>  
>  3. I tried saving binary maps both from ROIeditor and DTIstudio but
>  DTIstudio can't open any of them. Beside, DTIstudio doesn't produce the
>  same files as ROIeditor. The extensions are different and rois from
>  DTIstudio have lines for the operation while rois from ROIeditor 
> don't. I
>  tried adding those lines to the ".map" file of ROIeditor, without success.
>  
>  Can you give me some hint how to perform my task.
>  
>  Software versions:
>  Roieditor v1.5 - 64bit
>  DTIstudio v3.03 Sep 2010 - 64bit
>  
>  Thank you. 
> _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 

From bhaas at uga.edu  Sun Sep  2 14:45:43 2012
From: bhaas at uga.edu (Brian Haas)
Date: Sun, 02 Sep 2012 18:45:43 -0000
Subject: [Mristudio-users] quality .flg file ?
Message-ID: <908A5928-89E2-4127-885E-0FC34075736F@uga.edu>

Hi All,
  I am interested in quantifying the number of slices that were removed during preprocessing (i.e., the number of slices stored in the quality .flg file).

Is there a way to open up the .flg file to simply count the number of slices removed (either within or out of DTIstudio)?

I hope to not have to open up each subject though DTIstudio and scrolling through all of the data to count the slices removed.

Any help or advice is greatly appreciated!

Thanx.

Brian


Brian W. Haas, Ph.D.
Assistant Professor
Department of Psychology
University of Georgia
Office: Psychology 522

Gene-Brain-Social Behavior Lab
http://psychology.uga.edu/gbsb

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From alb.net at gmail.com  Fri Nov 30 14:52:48 2012
From: alb.net at gmail.com (Dorian P.)
Date: Fri, 30 Nov 2012 14:52:48 -0500
Subject: [Mristudio-users] DTI normalization with Diffeomap on lesioned
	brains
Message-ID: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>

Hi all,

I am interested on normalizing lesioned brains with a dual channel
Diffeomap procedure. The normalization will be done on MNI existing
template of Diffeomap. Lesions typically come from surgical resections.

Does this procedure work well on lesioned brains or shall I need some mask
for Diffeomap to avoid normalizing the lesioned area?

Any comment is welcome. I couldn't find much about the topic on previous
posts and articles.

Thank you.
Dorian P
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From susumu at mri.jhu.edu  Fri Nov 30 17:54:55 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 30 Nov 2012 17:54:55 -0500
Subject: [Mristudio-users] DTI normalization with Diffeomap on lesioned
 brains
In-Reply-To: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>
References: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>
Message-ID: <CAEq9apJa3u6tr7bG8ivLXTCcf=6Hui00AZoJt9TPrk-bsg199g@mail.gmail.com>

In general, lesions (severe intensity changes) or severe anatomical changes
(e.g. missing tissues or tumor) are very difficult to deal with, when you
are using a transformation-based analysis.

When you use transformation with low elasticity (e.g. linear
transformation), the transformation could be less affected because the
registration would be mostly driven by the brain outlines. So, if your
lesions (intensity changes) do not accompany anatomical deformation, you
may be able to compare patients and controls.

As the elasticity increases, the transformation would be more affected by
the lesions. Of course, if the lesions are small, they may not cause much
problems but I assume you have large lesions.

If you are studying, for example, stroke and interested in anatomical
changes of contralateral hemisphere (or the brainstem), you can mask-out
the ipsilateral hemisphere for both patients and the atlas. We have done
this type of analyses before.

Sorry that I could give you only a generic answer. This is an issue that
the whole community faces.

On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <alb.net at gmail.com> wrote:

> Hi all,
>
> I am interested on normalizing lesioned brains with a dual channel
> Diffeomap procedure. The normalization will be done on MNI existing
> template of Diffeomap. Lesions typically come from surgical resections.
>
> Does this procedure work well on lesioned brains or shall I need some mask
> for Diffeomap to avoid normalizing the lesioned area?
>
> Any comment is welcome. I couldn't find much about the topic on previous
> posts and articles.
>
> Thank you.
> Dorian P
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From alb.net at gmail.com  Fri Nov 30 19:54:56 2012
From: alb.net at gmail.com (Dorian P.)
Date: Fri, 30 Nov 2012 19:54:56 -0500
Subject: [Mristudio-users] DTI normalization with Diffeomap on lesioned
 brains
In-Reply-To: <CAEq9apJa3u6tr7bG8ivLXTCcf=6Hui00AZoJt9TPrk-bsg199g@mail.gmail.com>
References: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>
	<CAEq9apJa3u6tr7bG8ivLXTCcf=6Hui00AZoJt9TPrk-bsg199g@mail.gmail.com>
Message-ID: <CAF9pfmZvhKY=M8PuneVN9xFOFFKBrWK+34Tx_z=+ikvR8nm3WA@mail.gmail.com>

Thank you for answering Dr. Mori,

Would it be feasible to mask only the lesion on the patient or does it have
to be on both patient and atlas?

Has anybody compared a T1 normalization on SPM and applying the matrix to
DTI to a low elasticity normalization in DTIstudio?

Best regards.
Dorian


2012/11/30 susumu mori <susumu at mri.jhu.edu>

> In general, lesions (severe intensity changes) or severe anatomical
> changes (e.g. missing tissues or tumor) are very difficult to deal with,
> when you are using a transformation-based analysis.
>
> When you use transformation with low elasticity (e.g. linear
> transformation), the transformation could be less affected because the
> registration would be mostly driven by the brain outlines. So, if your
> lesions (intensity changes) do not accompany anatomical deformation, you
> may be able to compare patients and controls.
>
> As the elasticity increases, the transformation would be more affected by
> the lesions. Of course, if the lesions are small, they may not cause much
> problems but I assume you have large lesions.
>
> If you are studying, for example, stroke and interested in anatomical
> changes of contralateral hemisphere (or the brainstem), you can mask-out
> the ipsilateral hemisphere for both patients and the atlas. We have done
> this type of analyses before.
>
> Sorry that I could give you only a generic answer. This is an issue that
> the whole community faces.
>
> On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Hi all,
>>
>> I am interested on normalizing lesioned brains with a dual channel
>> Diffeomap procedure. The normalization will be done on MNI existing
>> template of Diffeomap. Lesions typically come from surgical resections.
>>
>> Does this procedure work well on lesioned brains or shall I need some
>> mask for Diffeomap to avoid normalizing the lesioned area?
>>
>> Any comment is welcome. I couldn't find much about the topic on previous
>> posts and articles.
>>
>> Thank you.
>> Dorian P
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From susumu at mri.jhu.edu  Sat Dec  1 07:53:02 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 01 Dec 2012 07:53:02 -0500
Subject: [Mristudio-users] DTI normalization with Diffeomap on lesioned
 brains
In-Reply-To: <CAF9pfmZvhKY=M8PuneVN9xFOFFKBrWK+34Tx_z=+ikvR8nm3WA@mail.gmail.com>
References: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>
	<CAEq9apJa3u6tr7bG8ivLXTCcf=6Hui00AZoJt9TPrk-bsg199g@mail.gmail.com>
	<CAF9pfmZvhKY=M8PuneVN9xFOFFKBrWK+34Tx_z=+ikvR8nm3WA@mail.gmail.com>
Message-ID: <CAEq9apJXM34jdx==2nq-5H5=xUwdCgpsXbeH-ZHHqSNWszqCsQ@mail.gmail.com>

You need to mask anatomically equivalent regions in both the patients and
the atlas, which is difficult.
I assume your "lesions" mean surgically removed tissues. Is it correct? If
you can assume that the anatomical deformation around the lesions is small
(like the partial moon), you can register the patient image to the atlas by
affine (either automatically or landmark-driven) and transfer the lesion
locations to the atlas manually, I think. In stead of affine, you may be
able to use low-elasticity LDDMM (alpha = about 0.01).

I didn't quite get your second question. Using LDDMM (DiffeoMap), you can
control the elasticity by alpha value. 0.01 and larger give low elasticity.
0.005 is recommended for normal brains. 0.001-0.002 is used when anatomical
difference is large.

When you want alpha smaller than 0.005, cascading alphas are recommended
(e.g. three consecutive LDDMM with 0.01-0.005-0.002) to avoid being trapped
by a local minima. Using this cascading-alpha approach, you can also obtain
the intermediate results; results with low elasticity (alpha = 0.01),
medium alpha (alpha = 0.01/0.005).

In DiffeoMap, you can use up to 3 cascading alphas.

On Fri, Nov 30, 2012 at 7:54 PM, Dorian P. <alb.net at gmail.com> wrote:

> Thank you for answering Dr. Mori,
>
> Would it be feasible to mask only the lesion on the patient or does it
> have to be on both patient and atlas?
>
> Has anybody compared a T1 normalization on SPM and applying the matrix to
> DTI to a low elasticity normalization in DTIstudio?
>
> Best regards.
> Dorian
>
>
> 2012/11/30 susumu mori <susumu at mri.jhu.edu>
>
>> In general, lesions (severe intensity changes) or severe anatomical
>> changes (e.g. missing tissues or tumor) are very difficult to deal with,
>> when you are using a transformation-based analysis.
>>
>> When you use transformation with low elasticity (e.g. linear
>> transformation), the transformation could be less affected because the
>> registration would be mostly driven by the brain outlines. So, if your
>> lesions (intensity changes) do not accompany anatomical deformation, you
>> may be able to compare patients and controls.
>>
>> As the elasticity increases, the transformation would be more affected by
>> the lesions. Of course, if the lesions are small, they may not cause much
>> problems but I assume you have large lesions.
>>
>> If you are studying, for example, stroke and interested in anatomical
>> changes of contralateral hemisphere (or the brainstem), you can mask-out
>> the ipsilateral hemisphere for both patients and the atlas. We have done
>> this type of analyses before.
>>
>> Sorry that I could give you only a generic answer. This is an issue that
>> the whole community faces.
>>
>> On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <alb.net at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I am interested on normalizing lesioned brains with a dual channel
>>> Diffeomap procedure. The normalization will be done on MNI existing
>>> template of Diffeomap. Lesions typically come from surgical resections.
>>>
>>> Does this procedure work well on lesioned brains or shall I need some
>>> mask for Diffeomap to avoid normalizing the lesioned area?
>>>
>>> Any comment is welcome. I couldn't find much about the topic on previous
>>> posts and articles.
>>>
>>> Thank you.
>>> Dorian P
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From alb.net at gmail.com  Sat Dec  1 09:22:23 2012
From: alb.net at gmail.com (Dorian P.)
Date: Sat, 01 Dec 2012 09:22:23 -0500
Subject: [Mristudio-users] DTI normalization with Diffeomap on lesioned
 brains
In-Reply-To: <CAEq9apJXM34jdx==2nq-5H5=xUwdCgpsXbeH-ZHHqSNWszqCsQ@mail.gmail.com>
References: <CAF9pfmZeA1R3OKwNqdfb0jLpfwRw16Or9E23n07KOKn+Tz198A@mail.gmail.com>
	<CAEq9apJa3u6tr7bG8ivLXTCcf=6Hui00AZoJt9TPrk-bsg199g@mail.gmail.com>
	<CAF9pfmZvhKY=M8PuneVN9xFOFFKBrWK+34Tx_z=+ikvR8nm3WA@mail.gmail.com>
	<CAEq9apJXM34jdx==2nq-5H5=xUwdCgpsXbeH-ZHHqSNWszqCsQ@mail.gmail.com>
Message-ID: <CAF9pfmbufqRetXcHMU8p23XF=LGeaegtcHJCtcAAyVgyYQ49fg@mail.gmail.com>

Thank you Dr. Mori,

Yes, my lesions are mostly surgical resections. The second question was
mostly a comparison between different alpha maps in LDDMM and SPM
normalization on lesioned brains. In SPM a T1 can be normalized (either
directly or through segmentation) on a MNI template and the transformation
matrix can be applied to any volume (i.e. BOLD, FA, Tensors). I was
wondering whether this method maybe worst or better on lesioned data
compared to LDDMM.

Best regards.
Dorian

2012/12/1 susumu mori <susumu at mri.jhu.edu>

> You need to mask anatomically equivalent regions in both the patients and
> the atlas, which is difficult.
> I assume your "lesions" mean surgically removed tissues. Is it correct? If
> you can assume that the anatomical deformation around the lesions is small
> (like the partial moon), you can register the patient image to the atlas by
> affine (either automatically or landmark-driven) and transfer the lesion
> locations to the atlas manually, I think. In stead of affine, you may be
> able to use low-elasticity LDDMM (alpha = about 0.01).
>
> I didn't quite get your second question. Using LDDMM (DiffeoMap), you can
> control the elasticity by alpha value. 0.01 and larger give low elasticity.
> 0.005 is recommended for normal brains. 0.001-0.002 is used when anatomical
> difference is large.
>
> When you want alpha smaller than 0.005, cascading alphas are recommended
> (e.g. three consecutive LDDMM with 0.01-0.005-0.002) to avoid being trapped
> by a local minima. Using this cascading-alpha approach, you can also obtain
> the intermediate results; results with low elasticity (alpha = 0.01),
> medium alpha (alpha = 0.01/0.005).
>
> In DiffeoMap, you can use up to 3 cascading alphas.
>
>
> On Fri, Nov 30, 2012 at 7:54 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Thank you for answering Dr. Mori,
>>
>> Would it be feasible to mask only the lesion on the patient or does it
>> have to be on both patient and atlas?
>>
>> Has anybody compared a T1 normalization on SPM and applying the matrix to
>> DTI to a low elasticity normalization in DTIstudio?
>>
>> Best regards.
>> Dorian
>>
>>
>> 2012/11/30 susumu mori <susumu at mri.jhu.edu>
>>
>>> In general, lesions (severe intensity changes) or severe anatomical
>>> changes (e.g. missing tissues or tumor) are very difficult to deal with,
>>> when you are using a transformation-based analysis.
>>>
>>> When you use transformation with low elasticity (e.g. linear
>>> transformation), the transformation could be less affected because the
>>> registration would be mostly driven by the brain outlines. So, if your
>>> lesions (intensity changes) do not accompany anatomical deformation, you
>>> may be able to compare patients and controls.
>>>
>>> As the elasticity increases, the transformation would be more affected
>>> by the lesions. Of course, if the lesions are small, they may not cause
>>> much problems but I assume you have large lesions.
>>>
>>> If you are studying, for example, stroke and interested in anatomical
>>> changes of contralateral hemisphere (or the brainstem), you can mask-out
>>> the ipsilateral hemisphere for both patients and the atlas. We have done
>>> this type of analyses before.
>>>
>>> Sorry that I could give you only a generic answer. This is an issue that
>>> the whole community faces.
>>>
>>> On Fri, Nov 30, 2012 at 2:52 PM, Dorian P. <alb.net at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am interested on normalizing lesioned brains with a dual channel
>>>> Diffeomap procedure. The normalization will be done on MNI existing
>>>> template of Diffeomap. Lesions typically come from surgical resections.
>>>>
>>>> Does this procedure work well on lesioned brains or shall I need some
>>>> mask for Diffeomap to avoid normalizing the lesioned area?
>>>>
>>>> Any comment is welcome. I couldn't find much about the topic on
>>>> previous posts and articles.
>>>>
>>>> Thank you.
>>>> Dorian P
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing list
>>>> mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> mristudio-users-unsubscribe at mristudio.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From marta.varela at kcl.ac.uk  Wed Dec  5 12:10:32 2012
From: marta.varela at kcl.ac.uk (Marta Varela)
Date: Wed, 05 Dec 2012 17:10:32 +0000
Subject: [Mristudio-users] Format of FA and Principal Vector Files for Fiber
	Tracking
Message-ID: <50BF8008.3020609@kcl.ac.uk>

Hi.

I would like to use the "Continuous Fiber Tracking using principal 
vector and FA map" tool, but cannot find any information as to the 
format of the input files. I am not familiar with .ani and .vec files 
and could not find any information on the structure of the .dat file.

Can you please let me know how I should write my x*y*z FA image and 
x*y*z*3 principal vector image to be read by DTI Studio?

Many thanks. Best wishes,
Marta



From susumu at mri.jhu.edu  Thu Dec  6 14:10:34 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Thu, 06 Dec 2012 14:10:34 -0500
Subject: [Mristudio-users] Format of FA and Principal Vector Files for
 Fiber Tracking
In-Reply-To: <50BF8008.3020609@kcl.ac.uk>
References: <50BF8008.3020609@kcl.ac.uk>
Message-ID: <CAEq9apLnDFvx_W+cEy3tVOXhD_8gB93ATe6z7uw3HhpF+dPZgw@mail.gmail.com>

Hi Marta,

I admit that it is confusing.
The two files needed for the fiber tracking (*.ani and *.vec) is labeled as
FA and eigenvector0 in DtiStudio.
If you are using DtiStudio to process your data, it saves various images
after the tensor calculation, which should include these FA and
eigenvector0 files.

Susumu

On Wed, Dec 5, 2012 at 12:10 PM, Marta Varela <marta.varela at kcl.ac.uk>wrote:

> Hi.
>
> I would like to use the "Continuous Fiber Tracking using principal
> vector and FA map" tool, but cannot find any information as to the
> format of the input files. I am not familiar with .ani and .vec files
> and could not find any information on the structure of the .dat file.
>
> Can you please let me know how I should write my x*y*z FA image and
> x*y*z*3 principal vector image to be read by DTI Studio?
>
> Many thanks. Best wishes,
> Marta
>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
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From cfigley at gmail.com  Sat Dec  8 19:35:56 2012
From: cfigley at gmail.com (Chase Figley)
Date: Sat, 08 Dec 2012 19:35:56 -0500
Subject: [Mristudio-users] LDDMM Kimap problems
Message-ID: <CAFn7RgPQyxR78c6MywzGkfvSXGEf1LCo3=fGE9BwLRFBED6-fw@mail.gmail.com>

Hi LDDMM and DiffeoMap Experts,

I have uploaded a few datasets to the LDDMM server over the past week and
have successfully retried my results.  However, when I apply the Kimap.vtk
to my linearly normalized AIR images (skull stripped mean b0), I don't see
any changes in my updated "lddmm" images.  And similarly, when I combine my
AIR and Kimap.vtk files to generate an "OverallKimap", the images come out
looking the same as the linearly normalized AIR images.

This is particularly obvious in some of my older subjects who have large
ventricles.  While the outer dimensions of their brains look fine, the
subcortical structures are clearly not properly aligned, so this leads me
to believe that there is something wrong with my Kimap.vtk files.

Does anyone know what might be happening here (and/or have any
recommendations)?  Has anyone else had a problem like this lately?

In case it matters, I have tried to use all of the default settings, except
I used the three-step elasticity option (alpha = 0.01, 0.005, 0.002).
However, I am a Mac user who has been doing things through a virtual
machine, and since DiffeoMap will not create the process.md5 file
correctly, I have been doing the last few steps (i.e., creating the md5sum,
and uploading to the server through the Terminal).  I thought everything
would have worked fine because I was able to upload and download my data,
but could this be causing any problems?

Thanks in advance for any help/advice,

Chase

-- 
Chase Figley, PhD
Johns Hopkins University
Department of Neuroscience
Department of Psychological and Brain Sciences
F.M. Kirby Research Center for Functional Brain Imaging
http://sites.google.com/site/cfigley/
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From susumu at mri.jhu.edu  Sat Dec  8 21:37:16 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sat, 08 Dec 2012 21:37:16 -0500
Subject: [Mristudio-users] LDDMM Kimap problems
In-Reply-To: <CAFn7RgPQyxR78c6MywzGkfvSXGEf1LCo3=fGE9BwLRFBED6-fw@mail.gmail.com>
References: <CAFn7RgPQyxR78c6MywzGkfvSXGEf1LCo3=fGE9BwLRFBED6-fw@mail.gmail.com>
Message-ID: <CAEq9ap+TFVRO4a2SLyjUZQFj0z1KXG_dJpXAfsHEsdixZNEPgw@mail.gmail.com>

Hi Chase,

We'll keep our eyes on reports from other users. If this is an isolated
case, I suspect there is a procedural error.
Please check Template and Target images that were included in the returned
results.
Make sure that these images are what you meant (Template = atlas, Target =
your image).
Maybe these two images are identical (thus no transformation) for some
reason.

Also, please check the text files in the results and make sure your alpha
values were really 0.01, 0.005, 0.002.

Susumu

On Sat, Dec 8, 2012 at 7:35 PM, Chase Figley <cfigley at gmail.com> wrote:

> Hi LDDMM and DiffeoMap Experts,
>
> I have uploaded a few datasets to the LDDMM server over the past week and
> have successfully retried my results.  However, when I apply the Kimap.vtk
> to my linearly normalized AIR images (skull stripped mean b0), I don't see
> any changes in my updated "lddmm" images.  And similarly, when I combine my
> AIR and Kimap.vtk files to generate an "OverallKimap", the images come out
> looking the same as the linearly normalized AIR images.
>
> This is particularly obvious in some of my older subjects who have large
> ventricles.  While the outer dimensions of their brains look fine, the
> subcortical structures are clearly not properly aligned, so this leads me
> to believe that there is something wrong with my Kimap.vtk files.
>
> Does anyone know what might be happening here (and/or have any
> recommendations)?  Has anyone else had a problem like this lately?
>
> In case it matters, I have tried to use all of the default settings,
> except I used the three-step elasticity option (alpha = 0.01, 0.005,
> 0.002).  However, I am a Mac user who has been doing things through a
> virtual machine, and since DiffeoMap will not create the process.md5 file
> correctly, I have been doing the last few steps (i.e., creating the md5sum,
> and uploading to the server through the Terminal).  I thought everything
> would have worked fine because I was able to upload and download my data,
> but could this be causing any problems?
>
> Thanks in advance for any help/advice,
>
> Chase
>
> --
> Chase Figley, PhD
> Johns Hopkins University
> Department of Neuroscience
> Department of Psychological and Brain Sciences
> F.M. Kirby Research Center for Functional Brain Imaging
> http://sites.google.com/site/cfigley/
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From 107310 at ib.k.u-tokyo.ac.jp  Fri Dec 14 04:07:15 2012
From: 107310 at ib.k.u-tokyo.ac.jp (=?ISO-2022-JP?B?GyRCREQhIU1IGyhC?=)
Date: Fri, 14 Dec 2012 18:07:15 +0900
Subject: [Mristudio-users] How to use Skull Stripping in ROIEditor
Message-ID: <1355476035475228.107305739@ums005.ecc.u-tokyo.ac.jp>

Hi DTI experts


I would like to use the skull stripping function in ROIEditor, 
so that I am doing statistical processing in MATLAB environment.

I have the human brain trace map data in analyze format made by DTI-studio as following parameters:
256 x 256 x 40 slices, 26 image blocks (Siemens mosaic).
The skull is supposed to prevent the normalize processing in MATLAB.


Please help me with this.
I'll appreciate your help.

Sincerely,

*********************************************
Department of Integrated Biosciences
Graduate School of Fronteir Sciences
The University of Tokyo
5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
Tel.             +81 4 7136 3634            

YO CHIN
Email; 107310 at ib.k.u-tokyo.ac.jp
*********************************************

From Saaussan.Madi at bruker-biospin.com  Thu Dec  6 14:13:40 2012
From: Saaussan.Madi at bruker-biospin.com (Madi, Saaussan)
Date: Thu, 06 Dec 2012 14:13:40 -0500
Subject: [Mristudio-users] Can DTI studio read Bruker (4Byte signed integer
	data)
Message-ID: <4B2FF0449FE9594AA4B5739315B37B24875501@EXCH1USA.bbious.ads.bruker.de>

Hi,

Can DTI studio read Bruker (PV5.1) (4Byte signed integer data)?

 

Best Regards,

Saaussan

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From xli16 at jhmi.edu  Fri Dec 14 10:35:53 2012
From: xli16 at jhmi.edu (Xin Li)
Date: Fri, 14 Dec 2012 10:35:53 -0500
Subject: [Mristudio-users] How to use Skull Stripping in ROIEditor
Message-ID: <7110b21032e51.50cb0109@johnshopkins.edu>

Please look at the attached screen shots.

If you want to skull strip one image, choose the "Skull strip the current active image only" option.

If you want to skull strip several images, there are two methods to do it.

1. Choose the "Skull strip the loaded images using the current active image as the template" option
2. Skull strip one image. Use the mask binary file created by DiffeoMap and the threshold function to generate a roi object. Then use the mask function to apply this roi object to other loaded images.

I recommend the second method. In general, the skull stripping function of ROIEditor will yield good results for b0 images with default parameter values. My colleagues usually skull strip B0 first and then use the second method to skull strip other images, for example, T2, T1...

There are some explanation about the parameters of the skull stripping function at 
https://www.mristudio.org/wiki/faq#head-a48a884070667bf76e504e119c05a63299e56d66
Please take a look.


Xin

----- Original Message -----
From: ??? <107310 at ib.k.u-tokyo.ac.jp>
Date: Friday, December 14, 2012 4:07 am
Subject: [Mristudio-users] How to use Skull Stripping in ROIEditor
To: mristudio-users at mristudio.org


> Hi DTI experts
>  
>  
>  I would like to use the skull stripping function in ROIEditor, 
>  so that I am doing statistical processing in MATLAB environment.
>  
>  I have the human brain trace map data in analyze format made by 
> DTI-studio as following parameters:
>  256 x 256 x 40 slices, 26 image blocks (Siemens mosaic).
>  The skull is supposed to prevent the normalize processing in MATLAB.
>  
>  
>  Please help me with this.
>  I'll appreciate your help.
>  
>  Sincerely,
>  
>  *********************************************
>  Department of Integrated Biosciences
>  Graduate School of Fronteir Sciences
>  The University of Tokyo
>  5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
>  Tel.             +81 4 7136 3634            
>  
>  YO CHIN
>  Email; 107310 at ib.k.u-tokyo.ac.jp
>  *********************************************
>  _______________________________________________
>  mristudio-users mailing list
>  mristudio-users at mristudio.org
>  
>  Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org 
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From susumu at mri.jhu.edu  Fri Dec 14 21:34:10 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Fri, 14 Dec 2012 21:34:10 -0500
Subject: [Mristudio-users] Can DTI studio read Bruker (4Byte signed
 integer data)
In-Reply-To: <4B2FF0449FE9594AA4B5739315B37B24875501@EXCH1USA.bbious.ads.bruker.de>
References: <4B2FF0449FE9594AA4B5739315B37B24875501@EXCH1USA.bbious.ads.bruker.de>
Message-ID: <CAEq9apKpFQ-_HohHD5DftBJNQcCoZLtFBrmkfEwst3pr_J0uiA@mail.gmail.com>

We have been routinely analyzing Bruker data here.
We'll send you more specific information shortly.

On Thu, Dec 6, 2012 at 2:13 PM, Madi, Saaussan <
Saaussan.Madi at bruker-biospin.com> wrote:

> Hi,****
>
> Can DTI studio read Bruker (PV5.1) (4Byte signed integer data)?****
>
> ** **
>
> Best Regards,****
>
> Saaussan****
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From jirey at mail.usf.edu  Tue Dec 18 15:36:29 2012
From: jirey at mail.usf.edu (Jose Rey)
Date: Tue, 18 Dec 2012 15:36:29 -0500
Subject: [Mristudio-users] Agilent / Varian Preclinical DTI: anybody out
	there?
Message-ID: <CANgw47+__=0zjY=u_dj6_4N+LKKP39dedjh7DYy5g3G=9ANNdw@mail.gmail.com>

Hi,

Is anybody using DTI studio to analyze DTI from Varian/Agilent Preclinical
systems?  The VNMRJ (Agilent's software) can do some pre-processing.
 However, the formatting of the data doesn't seem to be compatible with any
of the inputs for DTI studio.

Thank you very much,

Jose I. Rey
University of South Florida
Moffitt Cancer Center
Tampa, FL
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From Mark.Wagshul at einstein.yu.edu  Tue Dec 18 23:04:35 2012
From: Mark.Wagshul at einstein.yu.edu (Mark Wagshul)
Date: Wed, 19 Dec 2012 04:04:35 +0000
Subject: [Mristudio-users] Agilent / Varian Preclinical DTI: anybody
	out	there?
In-Reply-To: <CANgw47+__=0zjY=u_dj6_4N+LKKP39dedjh7DYy5g3G=9ANNdw@mail.gmail.com>
References: <CANgw47+__=0zjY=u_dj6_4N+LKKP39dedjh7DYy5g3G=9ANNdw@mail.gmail.com>
Message-ID: <14DC0AB8AE8F734CAD5FC876B36AEFF61F87C39B@YUWEXCPM11.yuad.uds.yu.edu>

We have software which reads in the data and outputs it in binary format, which can be read under the "Philips" format in DTIStudio.

Mark

_______________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011<tel:718-430-4011>
Email: mark.wagshul at einstein.yu.edu<mailto:mark.wagshul at einstein.yu.edu>

[Einstein_LogoTagA_Blue_RGB]


From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jose Rey
Sent: Tuesday, December 18, 2012 3:36 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: [Mristudio-users] Agilent / Varian Preclinical DTI: anybody out there?

Hi,

Is anybody using DTI studio to analyze DTI from Varian/Agilent Preclinical systems?  The VNMRJ (Agilent's software) can do some pre-processing.  However, the formatting of the data doesn't seem to be compatible with any of the inputs for DTI studio.

Thank you very much,

Jose I. Rey
University of South Florida
Moffitt Cancer Center
Tampa, FL
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From albnet at gmail.com  Fri Dec 21 13:08:13 2012
From: albnet at gmail.com (Anonim)
Date: Fri, 21 Dec 2012 13:08:13 -0500
Subject: [Mristudio-users] Fiber tracking option 1 or 2 ?
Message-ID: <CAF9pfmYHZA96T2gM4RvF488O1yN1HhxJ2rAHH1AiJcRQ1rjDig@mail.gmail.com>

Hi guys,

Are the two options in fiber tracking equivalent:
Option 1: FA + principal vector (eigenvector)
Option 2: Tensor image

If not, what is the difference?

Thank you.

Dorian
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From alb.net at gmail.com  Wed Dec 26 12:16:26 2012
From: alb.net at gmail.com (Dorian P.)
Date: Wed, 26 Dec 2012 12:16:26 -0500
Subject: [Mristudio-users] Gradient tables and SPM coregistration
Message-ID: <CAF9pfmZPASZpOZXeZWRocR4Rc2GVGEfsaA77SHNJgXrOwPE9=A@mail.gmail.com>

Hi everybody, and happy holidays,

I am using DTIstudio in a complex workflow.

First, I need to make a nonlinear registration using masks on lesioned
data. SPM is doing a good job at this point. To apply the transformation
matrix produced by SPM, I must export images from DTI studio (analyze
format), apply the deformations in SPM and import the files back to
DTIstudio. However I am not sure whether a problem arises with the gradient
tables not being the same any more. How can I apply the transformation
matrix from SPM? Is there maybe a way to convert .mat files to .vtk and do
all transofmrations in DTIstudio/Diffeomap?


Second, having both T1 and b0 images in two different sessions, which one
is better in theory for registration, T1s or B0s ? In many examples the b0
has been used for linear (AIR) and nonlinear (LBBDMM) registration. But on
the other side a b0 is acquired in a fraction of the time of a T1, so may
be less stable to artifacts (or with fat artifacts?).

Thank you.
Dorian
TJU
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From susumu at mri.jhu.edu  Sun Dec 30 10:16:03 2012
From: susumu at mri.jhu.edu (susumu mori)
Date: Sun, 30 Dec 2012 10:16:03 -0500
Subject: [Mristudio-users] Gradient tables and SPM coregistration
In-Reply-To: <CAF9pfmZPASZpOZXeZWRocR4Rc2GVGEfsaA77SHNJgXrOwPE9=A@mail.gmail.com>
References: <CAF9pfmZPASZpOZXeZWRocR4Rc2GVGEfsaA77SHNJgXrOwPE9=A@mail.gmail.com>
Message-ID: <CAEq9apLT0LEFnK7-3OqR0aUVWKfeyU-T-5Va5mQ9+YuWctJV4w@mail.gmail.com>

Hi Dorian,

We don't have experience in mixing SPM transformation and MriStudio
pipeline. In general, you have to be very careful to mix pipelines from
different sources;

1) coordinate systems could be different; right-hand or left-hand
coordinates / neurology or radiology orientation. You have to be careful so
that the images and transformation matrices are in correct orders.
2) gradient vector re-orientation: If you touch raw diffusion-weighted
images, you have to transform the gradient vectors too. This is not
difficult when you use linear transformation, but if you are using
non-linear transformation, each voxel has to have its own gradient table.
The procedure becomes simpler if you transform images after tensor
calculation, but if you transform a tensor field, you need to make sure to
re-orient the tensor in each voxel.

In general, each software (FSL, SPM, MriStudio) should be already tested
for the consistency for these issues in a transparent manner, but once you
mix the pipeline, such a consistency may be lost.

Susumu

On Wed, Dec 26, 2012 at 12:16 PM, Dorian P. <alb.net at gmail.com> wrote:

> Hi everybody, and happy holidays,
>
> I am using DTIstudio in a complex workflow.
>
> First, I need to make a nonlinear registration using masks on lesioned
> data. SPM is doing a good job at this point. To apply the transformation
> matrix produced by SPM, I must export images from DTI studio (analyze
> format), apply the deformations in SPM and import the files back to
> DTIstudio. However I am not sure whether a problem arises with the gradient
> tables not being the same any more. How can I apply the transformation
> matrix from SPM? Is there maybe a way to convert .mat files to .vtk and do
> all transofmrations in DTIstudio/Diffeomap?
>
>
> Second, having both T1 and b0 images in two different sessions, which one
> is better in theory for registration, T1s or B0s ? In many examples the b0
> has been used for linear (AIR) and nonlinear (LBBDMM) registration. But on
> the other side a b0 is acquired in a fraction of the time of a T1, so may
> be less stable to artifacts (or with fat artifacts?).
>
> Thank you.
> Dorian
> TJU
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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From alb.net at gmail.com  Mon Dec 31 14:31:36 2012
From: alb.net at gmail.com (Dorian P.)
Date: Mon, 31 Dec 2012 14:31:36 -0500
Subject: [Mristudio-users] Gradient tables and SPM coregistration
In-Reply-To: <CAEq9apLT0LEFnK7-3OqR0aUVWKfeyU-T-5Va5mQ9+YuWctJV4w@mail.gmail.com>
References: <CAF9pfmZPASZpOZXeZWRocR4Rc2GVGEfsaA77SHNJgXrOwPE9=A@mail.gmail.com>
	<CAEq9apLT0LEFnK7-3OqR0aUVWKfeyU-T-5Va5mQ9+YuWctJV4w@mail.gmail.com>
Message-ID: <CAF9pfmbNKzya9FUY7T12anbD-psFCgMMFo8S_dPNnTe+j6VhXw@mail.gmail.com>

Hi Dr. Mori,

I think I have figured out the pipeline now. Two more questions I have are:

1. I have tested both DTIstudio and ExploreDTI. The second produced
occasionally more voxels with FA over 0.25 following motion and eddy
current correction. As you have recently coauthored a paper with Dr.
Leemans (Diffusion tensor imaging and beyond), I wanted to ask what may be
different to cause different results from the same dataset.

2. You mentioned in another email the possibility to use masks (for
example, an entire hemisphere) during normalization. I haven't found an
option like this in Diffeomap. Is there any such possibility, so that I can
possibly avoid using SPM in the pipeline?

Thank you.
Dorian


2012/12/30 susumu mori <susumu at mri.jhu.edu>

> Hi Dorian,
>
> We don't have experience in mixing SPM transformation and MriStudio
> pipeline. In general, you have to be very careful to mix pipelines from
> different sources;
>
> 1) coordinate systems could be different; right-hand or left-hand
> coordinates / neurology or radiology orientation. You have to be careful so
> that the images and transformation matrices are in correct orders.
> 2) gradient vector re-orientation: If you touch raw diffusion-weighted
> images, you have to transform the gradient vectors too. This is not
> difficult when you use linear transformation, but if you are using
> non-linear transformation, each voxel has to have its own gradient table.
> The procedure becomes simpler if you transform images after tensor
> calculation, but if you transform a tensor field, you need to make sure to
> re-orient the tensor in each voxel.
>
> In general, each software (FSL, SPM, MriStudio) should be already tested
> for the consistency for these issues in a transparent manner, but once you
> mix the pipeline, such a consistency may be lost.
>
> Susumu
>
> On Wed, Dec 26, 2012 at 12:16 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Hi everybody, and happy holidays,
>>
>> I am using DTIstudio in a complex workflow.
>>
>> First, I need to make a nonlinear registration using masks on lesioned
>> data. SPM is doing a good job at this point. To apply the transformation
>> matrix produced by SPM, I must export images from DTI studio (analyze
>> format), apply the deformations in SPM and import the files back to
>> DTIstudio. However I am not sure whether a problem arises with the gradient
>> tables not being the same any more. How can I apply the transformation
>> matrix from SPM? Is there maybe a way to convert .mat files to .vtk and do
>> all transofmrations in DTIstudio/Diffeomap?
>>
>>
>> Second, having both T1 and b0 images in two different sessions, which one
>> is better in theory for registration, T1s or B0s ? In many examples the b0
>> has been used for linear (AIR) and nonlinear (LBBDMM) registration. But on
>> the other side a b0 is acquired in a fraction of the time of a T1, so may
>> be less stable to artifacts (or with fat artifacts?).
>>
>> Thank you.
>> Dorian
>> TJU
>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> mristudio-users-unsubscribe at mristudio.org
>>
>>
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
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