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

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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
>
> _______________________________________________
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>


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