From susumu at mri.jhu.edu  Fri Mar 20 11:25:25 2009
From: susumu at mri.jhu.edu (susumu)
Date: Fri, 20 Mar 2009 11:25:25 -0400
Subject: [Announcements] MriStudio Tutorial in ISMRM, Hawaii
Message-ID: <7k7ed7$6ppe84@ipex3.johnshopkins.edu>

Dear MriStudio / DtiStudio Users,

 

We are very happy to announce tutorial courses that will be held in The
Queen's Medical Center on 4/18 and 4/19, 10:00 am - 4:00 pm. This tutorial
will be held jointly with and made possible by Professor Linda Chang's lab
in University of Hawaii. 

 

The two courses on Sat (4/18) and Sun (4/19) will be the same and each day
will accommodate up to 40 people with a first-come-first-serve basis.  

 

As usual, the tutorial is free, but all attendants are responsible for all
costs associated with their trip and meal. In addition, you are required to
bring your own laptop computers, which are pre-conditioned by following the
procedures described in https://www.mristudio.org/wiki/Tutorial. The data
and software are too large to implement on the tutorial days. Please make
sure to implement all these resources, register your computer (for
Landmarker), and follow the test run described in the website.

 

If you are interested in attending the course, please forward , your name /
Institute / date you come, to xin_xu at mri.jhu.edu.

 

The precise location information will be announced soon. The tutorial site
will also be updated soon.

To avoid annoying users who are not interested in this tutorial, the
following announcement will be sent only to users who are registered to the
Mailing List.

 

See you soon in Hawaii,

 

Susumu Mori

 

 

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From neal.prakash at gmail.com  Fri Mar 20 20:50:21 2009
From: neal.prakash at gmail.com (neal.prakash at gmail.com)
Date: Fri, 20 Mar 2009 14:50:21 -1000
Subject: [Announcements] MriStudio Tutorial in ISMRM, Hawaii
In-Reply-To: <7k7ed7$6ppe84@ipex3.johnshopkins.edu>
References: <7k7ed7$6ppe84@ipex3.johnshopkins.edu>
Message-ID: <dbe7a7ef0903201750s2e1c9baeuc076fa14945c3771@mail.gmail.com>

Dear Susumu,

Thanks for putting on the tutorial! I very much wanted to
attend, unfortunately I will be out of town that weekend. When/where is your
next one? Do you have any new tools for probabilistic tract tracing?

Warmest regards,

-- 
Neal Prakash MD, PhD
http://groups.google.com/group/neal-prakash-md-phd




On 3/20/09, susumu <susumu at mri.jhu.edu> wrote:
>
>  Dear MriStudio / DtiStudio Users,
>
>
>
> We are very happy to announce tutorial courses that will be held in The
> Queen's Medical Center on 4/18 and 4/19, 10:00 am - 4:00 pm. This tutorial
> will be held jointly with and made possible by Professor Linda Chang's lab
> in University of Hawaii.
>
>
>
> The two courses on Sat (4/18) and Sun (4/19) will be the same and each day
> will accommodate up to 40 people with a first-come-first-serve basis.
>
>
>
> As usual, the tutorial is free, but all attendants are responsible for all
> costs associated with their trip and meal. In addition, you are required to
> bring your own laptop computers, which are pre-conditioned by following the
> procedures described in https://www.mristudio.org/wiki/Tutorial. The data
> and software are too large to implement on the tutorial days. Please make
> sure to implement all these resources, register your computer (for
> Landmarker), and follow the test run described in the website.
>
>
>
> If you are interested in attending the course, please forward , your name /
> Institute / date you come, to xin_xu at mri.jhu.edu.
>
>
>
> The precise location information will be announced soon. The tutorial site
> will also be updated soon.
>
> To avoid annoying users who are not interested in this tutorial, *the
> following announcement will be sent only to users who are registered to the
> Mailing List.*
>
> * *
>
> See you soon in Hawaii,
>
>
>
> Susumu Mori
>
>
>
>
>
> _______________________________________________
> Announcements mailing list
> Announcements at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/announcements
>
>
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From susumu at mri.jhu.edu  Tue Mar 31 11:25:45 2009
From: susumu at mri.jhu.edu (susumu)
Date: Tue, 31 Mar 2009 11:25:45 -0400
Subject: [Announcements] Tutorial in Hawaii
Message-ID: <7k7ed7$6tit5n@ipex3.johnshopkins.edu>

Dear DtiStudio / Landmarker / RoiEditor Users,

 

We still have a plenty of room (because we have two days this time) for the
free tutorial. 

 

This time, we will spend ample time for Landmarker / RoiEditor for automated
atlas-based and pixel-based quantitative analyses of DTI / MRI data. 

 

Please feel free to join the session in Hawaii!

 

Susumu Mori

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From tilakgattu at gmail.com  Tue Mar 31 11:32:44 2009
From: tilakgattu at gmail.com (ramtilak gattu)
Date: Tue, 31 Mar 2009 11:32:44 -0400
Subject: [Announcements] MriStudio Tutorial in ISMRM, Hawaii
In-Reply-To: <7k7ed7$6ppe84@ipex3.johnshopkins.edu>
References: <7k7ed7$6ppe84@ipex3.johnshopkins.edu>
Message-ID: <2802e1eb0903310832v248c15cftd6d4ce92692f5fce@mail.gmail.com>

Hi Xin,
Could you please register us for the training session

Name (s): Ramtilak Gattu, Zhifeng Kou & Randall R Benson
Institute: Wayne State University
Date of Arrival : 04/17/09


thanks

Regards
Tilak


On Fri, Mar 20, 2009 at 11:25 AM, susumu <susumu at mri.jhu.edu> wrote:

>  Dear MriStudio / DtiStudio Users,
>
>
>
> We are very happy to announce tutorial courses that will be held in The
> Queen's Medical Center on 4/18 and 4/19, 10:00 am - 4:00 pm. This tutorial
> will be held jointly with and made possible by Professor Linda Chang's lab
> in University of Hawaii.
>
>
>
> The two courses on Sat (4/18) and Sun (4/19) will be the same and each day
> will accommodate up to 40 people with a first-come-first-serve basis.
>
>
>
> As usual, the tutorial is free, but all attendants are responsible for all
> costs associated with their trip and meal. In addition, you are required to
> bring your own laptop computers, which are pre-conditioned by following the
> procedures described in https://www.mristudio.org/wiki/Tutorial. The data
> and software are too large to implement on the tutorial days. Please make
> sure to implement all these resources, register your computer (for
> Landmarker), and follow the test run described in the website.
>
>
>
> If you are interested in attending the course, please forward , your name /
> Institute / date you come, to xin_xu at mri.jhu.edu.
>
>
>
> The precise location information will be announced soon. The tutorial site
> will also be updated soon.
>
> To avoid annoying users who are not interested in this tutorial, *the
> following announcement will be sent only to users who are registered to the
> Mailing List.*
>
> * *
>
> See you soon in Hawaii,
>
>
>
> Susumu Mori
>
>
>
>
>
> _______________________________________________
> Announcements mailing list
> Announcements at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/announcements
>
>


-- 
Ramtilak Gattu M.S
Research Assistant
MR Research Facility
Wayne State University
ph:  313-993-8896 (MRRF-office)
     313-745-2487 (MS-office)
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From susumu at mri.jhu.edu  Tue Mar 31 11:48:49 2009
From: susumu at mri.jhu.edu (susumu)
Date: Tue, 31 Mar 2009 11:48:49 -0400
Subject: [Announcements] Tutorial
Message-ID: <7k7ed7$6tj7cl@ipex3.johnshopkins.edu>

Hi all,

 

Sorry that I forgot to mention.

 

If you are interested in the tutorial, please send reply to
Xin_Xu at mri.jhu.edu, not to the announcement at mristudio.org to avoid sending
emails to everybody.

 

To unsubscribe this mailing list, please go to
http://lists.mristudio.org/mailman/listinfo/mristudio-users

 

Thanks!

 

Susumu

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From support at mristudio.org  Thu May 14 11:36:46 2009
From: support at mristudio.org (support at mristudio.org)
Date: Thu, 14 May 2009 11:36:46 -0400 (EDT)
Subject: [Announcements] Release of of Landmarker1.5 and ROIEditor1.4
Message-ID: <1614.10.16.56.29.1242315406.squirrel@webmail.mristudio.org>

Dear Mristudio users,

We have released Landmarker 1.5 and ROIEditor 1.4. Please go to our website to
download them.

The new features are as follows:

Landmarker 1.5

1.The atlas sample images are updated. New WMPM data for ICBM_DTI_81 and
JHU_MNI_SS are added.

2.Users can do multiple alpha volume lddmm transformation. Users can enter up to
three differenct alpha values and get the corresponding Kimaps and Hmaps. For
example, if three alpha values are entered in order like 0.01, 0.005, 0.002, the
following Kimaps and the Hmaps are generated:
For the alpha value as 0.01: Kimap_01.vtk, Hmap_01.vtk
For the alpha value as 0.005: Kimap_005.vtk, Hmap_005.vtk
For the alpha value as 0.002: Kimap_002.vtk, Hmap_002.vtk
The overall transformation map: Kimap.vtk, Hmap.vtk

3. A potential numerical error related to tensor data transformation has been
fixed. Now the software can correctly handle tensor data with values less than
10^(-6).

4.Users can copy the current displayed image slice.

5.The process of landmark-based lddmm transformation is upgraded and can run
faster.

6.When the image data format is changed to byte or word, there are three
options: Automatic Scaling, Manual Scaling and No Scaling.

7.NIFTI images can be loaded to the software.


ROIEditor 1.4

1.The atlas sample images are updated. New WMPM data for ICBM_DTI_81 and
JHU_MNI_SS are added.

2.Users can exclude some pixels in statistical calculation by setting the range
of their intensities.

3.Users can copy the current displayed image slice.

4.Statistical data are displayed in four decimal points.

5.Users can grow or shrink a ROI object.

6.Users can export the vector values of the pixels contained in a ROI object.

7.Users can exclude some pixels when the pixel values are exported by setting
the range of their intensities.

8.NIFTI images can be loaded to the software.


If you have any questions about these two new softwares, please send your email
to Mristudio-users or support at mristudio.org.


Thanks!


Mristudio Support



From llanyon at eyecarecentre.org  Tue May 19 15:55:23 2009
From: llanyon at eyecarecentre.org (Linda Lanyon)
Date: Tue, 19 May 2009 12:55:23 -0700
Subject: [Announcements] subscribe
Message-ID: <033601c9d8bb$bfd6f730$58b75289@DC2NY2B1>

subscribe

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From support at mristudio.org  Fri May 29 11:23:17 2009
From: support at mristudio.org (support at mristudio.org)
Date: Fri, 29 May 2009 11:23:17 -0400 (EDT)
Subject: [Announcements] Online Manual of Landmarker
Message-ID: <2376.10.16.56.29.1243610597.squirrel@webmail.mristudio.org>

Dear MriStudio users,



Last year, we introduced two programs, Landmarker and RoiEditor. Landmarker lets
us normalize DTI data using linear and nonlinear (LDDMM) transformation based on
manually placed landmarks [1] or automatically [2, 3]. As you might have noticed
already, the manual of Landmarker in www.mristudio.org was quite minimum and
many of you have had hard time to learn how to use the software. We recently
updated the Lanamarker manual at
https://www.mristudio.org/wiki/user_manual/landmarker. Please see a section
called "Getting Started".



We are still working on more formal manuals but for a time being, we hope this
section will help you understand how the software works.



Sincerely,



Susumu Mori





[1] Zhang W, Li X, Zhang J, Luft A, Hanley DF, van Zijl P, Miller MI, Younes L,
Mori S, "Landmark-referenced voxel-based analysis of diffusion tensor images of
the brainstem white matter tracts; Application in patients with middle cereberal
artery stroke", Neuroimage, ePub



[2] Mori S., Oishi K., Jiang H, Jiang L., Li X., Akhter K., Hua K., Faria AV.,
Mahmod A., Woods R., Toga WA., Pike B, Rosa Neto P, Evans A, Zhang J, Huang H,
Miller MI, van Zijl, PCM, Mazziotta, J, "Stereotaxic white matter atlas based on
diffusion tensor imaging in an ICBM template", NeuroImage, 40, 570-582(2008)



[3] Oishi K, Faria A, Jiang H, Li X, Akhter K, Zhang J, Hsu J, Miller MI, van
Zijl PCM, 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 Alzheimers' disease participants", Neuroimage, ePub



From support at mristudio.org  Fri May 29 16:38:45 2009
From: support at mristudio.org (support at mristudio.org)
Date: Fri, 29 May 2009 16:38:45 -0400 (EDT)
Subject: [Announcements] Release of ROIEditor1.4.1
Message-ID: <3730.10.16.56.29.1243629525.squirrel@webmail.mristudio.org>

Mristudio users,

Recently a bug has been found in ROIEditor1.4. The feature "Exclude some pixels
by setting the range of their intensities" only works in the function
"Statistical Data for all ROI Objects in All Images". It doesn't work in other
related functions.

The bug has been fixed in the new version ROIEditor1.4.1. Now the feature also
works in the functions "Statistics for One ROI Object", "ROI Axial Profile",
"ROI Sagittal Profile", "ROI Coronal Profile" and "Export Pixel Value".

Please download the new version ROIEditor1.4.1 at our website.

If you have any questions about this new software, please send your email to
mristudio-users at mristudio.org.


Regards,


Xin


From susumu at mri.jhu.edu  Sun Aug 30 10:44:46 2009
From: susumu at mri.jhu.edu (susumu)
Date: Sun, 30 Aug 2009 10:44:46 -0400
Subject: [Announcements] Announcement for Forum
Message-ID: <AE5F586606BA416CBE04D7739636C005@SusumuThinkPad>

Dear MriStudio Users,

 

As you might have already noticed, we started a forum in www.mristudio.org
<http://www.mristudio.org/> . The mailing list is still active, but if you
prefer to use the forum, please don't hesitate to post your questions in the
forum. We will do our best to reply as early as possible.

 

To post your questions at the forum, it requires new registration but we
hope that it will enhance your experience with the MriStudio program family
(DtiStudio, RoiEditor, and Landmarker).

 

Also, we revised the documents for Landmarker and added a "Getting Started"
section (https://www.mristudio.org/wiki/user_manual/landmarker). Please try
this easy-to-follow procedure to learn DTI/MRI image normalization by this
program.

 

Sincerely,

 

Susumu Mori

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From susumu at mri.jhu.edu  Thu Sep 10 07:06:49 2009
From: susumu at mri.jhu.edu (susumu)
Date: Thu, 10 Sep 2009 07:06:49 -0400
Subject: [Announcements] Tutorials
Message-ID: <55A3DFB6648A498088AED2028951C58B@SusumuThinkPad>

Dear MriStudio Users,

 

Center of Brain Imaging Science will host the following tutorials in October
13th and November 14th. 

As usual, the tutorial is free, but you are expected to bring your own
laptop and cover all the travel expense by yourself.

 

Also, please make sure to install all programs and sample data and follow
the procedures explained at https://www.mristudio.org/wiki/Tutorial so that
your computer will be ready to follow the tutorial.

 

This time, we will spend more time (3 hours) on DTI data normalization and
quantification using Landmarker and RoiEditor, in addition to DtiStudio (3
hours). Following 2 papers should help understanding the quantification
strategy;

 

Mori S., Oishi K., Jiang H, Jiang L., Li X., Akhter K., Hua K., Faria AV.,
Mahmod A., Woods R., Toga WA., Pike B, Rosa Neto P, Evans A, Zhang J, Huang
H, Miller MI, van Zijl, PCM, Mazziotta, J, "Stereotaxic white matter atlas
based on diffusion tensor imaging in an ICBM template", NeuroImage, 40,
570-582(2008)

 

Oishi K, Faria A, Jiang H, Li X, Akhter K, Zhang J, Hsu J, Miller MI, van
Zijl PCM, 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 Alzheimers' disease participants", Neuroimage, 46, 486-499
(2009)

 

If you are interested in, please send an email to xin_xu at mri.jhu.edu.

 

Sincerely,

 

Susumu Mori

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

 

*  Johns Hopkins School of Medicine (Downtown Medical Campus), Baltimore, MD
10/13/2009 

*	Time: 10am - 5pm 

*         Location: Mountcastle Auditorium, the first floor of Preclinical
Training Building parking-map.pdf
<https://www.mristudio.org/wiki/Tutorial?action=AttachFile&do=get&target=par
king-map.pdf>  

*	Address: 725 N. Wolfe St., Baltimore 21205 

*  Kyoto University, Japan 11/14/2009 

*	Time: 1pm - 5pm 

*         Department of Radiology
<http://www.kuhp.kyoto-u.ac.jp/%7Ediag_rad/> 

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

 

 

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From support at mristudio.org  Fri Sep 18 16:10:24 2009
From: support at mristudio.org (support at mristudio.org)
Date: Fri, 18 Sep 2009 16:10:24 -0400 (EDT)
Subject: [Announcements] Release of DiffeoMap1.6 (previously known as
 Landmarker)
Message-ID: <2032.10.16.56.29.1253304624.squirrel@webmail.mristudio.org>

Mristudio users,

We would like to announce an important change of Landmarker. First of all,
Landmarker was renamed to DiffeoMap, to represent its function more accurately.
There are also few new functions added as listed below. Please go to our website
to download the latest DiffeoMap 1.6.

The new features of DiffeoMap 1.6 are:

1. After the transformations, the updated images can be automatically saved.

2. The buttons for all landmark-based transformations are moved to the tool panel.


If you have any questions about this new software, please send your email
to Mristudio-users or post in the forum in www.mristudio.org.


Thanks!


Mristudio Support



From xli at mristudio.org  Wed Nov  4 09:51:57 2009
From: xli at mristudio.org (xli at mristudio.org)
Date: Wed, 4 Nov 2009 09:51:57 -0500 (EST)
Subject: [Announcements] Tutorial in Kyoto Cancelled
Message-ID: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>

Dear MriStudio users,

Due to unavailability of Dr. Mori, the tutorial in Kyoto, Japan on 11/14 was
cancelled. We sincerely apologize this change. Please contact us
(xin_xu at mri.jhu.edu) if you have any question regarding this cancellation.

Sincerely


MriStudio Support


From HuangS4 at uthscsa.edu  Wed Nov  4 12:33:36 2009
From: HuangS4 at uthscsa.edu (Huang, Shiliang)
Date: Wed, 04 Nov 2009 11:33:36 -0600
Subject: [Announcements] How guarantee using the registered data to
	calculate the tensor?
In-Reply-To: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>
References: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>
Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCD83@HSC-M2.win.uthscsa.edu>

Hi everyone
I use AIR to do register. But how can I guarantee using the registered data to calculate the tensor? Because the original data and the registered data are all exist. I do not know my results derived from the original data or registered data.
Thanks
Shiliang

-----Original Message-----
From: announcements-bounces at mristudio.org [mailto:announcements-bounces at mristudio.org] On Behalf Of xli at mristudio.org
Sent: Wednesday, November 04, 2009 8:52 AM
To: announcements at mristudio.org
Subject: [Announcements] Tutorial in Kyoto Cancelled

Dear MriStudio users,

Due to unavailability of Dr. Mori, the tutorial in Kyoto, Japan on 11/14 was
cancelled. We sincerely apologize this change. Please contact us
(xin_xu at mri.jhu.edu) if you have any question regarding this cancellation.

Sincerely


MriStudio Support

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


From HuangS4 at uthscsa.edu  Wed Nov  4 14:39:38 2009
From: HuangS4 at uthscsa.edu (Huang, Shiliang)
Date: Wed, 04 Nov 2009 13:39:38 -0600
Subject: [Announcements] How to import two kinds of images
In-Reply-To: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>
References: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>
Message-ID: <54BCF36E4FE44644A377261164E3104548CD1BCDA0@HSC-M2.win.uthscsa.edu>

Hi Everyone
Thank you all very much. I want to register DTI data to the T1 image. How to import these two kinds of images?
Thanks
Shiliang

-----Original Message-----
From: announcements-bounces at mristudio.org [mailto:announcements-bounces at mristudio.org] On Behalf Of xli at mristudio.org
Sent: Wednesday, November 04, 2009 8:52 AM
To: announcements at mristudio.org
Subject: [Announcements] Tutorial in Kyoto Cancelled

Dear MriStudio users,

Due to unavailability of Dr. Mori, the tutorial in Kyoto, Japan on 11/14 was
cancelled. We sincerely apologize this change. Please contact us
(xin_xu at mri.jhu.edu) if you have any question regarding this cancellation.

Sincerely


MriStudio Support

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


From kakhter1 at jhu.edu  Wed Nov  4 17:18:05 2009
From: kakhter1 at jhu.edu (Kazi Dilruba Akhter)
Date: Wed, 04 Nov 2009 17:18:05 -0500
Subject: [Announcements] (no subject)
Message-ID: <4AF1FD9D.7040400@jhu.edu>



From caroarboleda at gmail.com  Wed Nov 11 09:51:28 2009
From: caroarboleda at gmail.com (Caro Arboleda)
Date: Wed, 11 Nov 2009 11:51:28 -0300
Subject: [Announcements] How guarantee using the registered data
	to	calculate the tensor?
In-Reply-To: <54BCF36E4FE44644A377261164E3104548CD1BCD83@HSC-M2.win.uthscsa.edu>
References: <2344.71.179.154.22.1257346317.squirrel@webmail.mristudio.org>
	<54BCF36E4FE44644A377261164E3104548CD1BCD83@HSC-M2.win.uthscsa.edu>
Message-ID: <5e0938400911110651j691dfb30i8f74c1c1503afaf@mail.gmail.com>

Good morning.

I am using DTIstudio to process some tree-trunk's images. My images are in
the Philips DICOM format.

I have several questions:

1. I used four different b factors (0, 100, 350 and 700). Which value should
I enter in the field "b_value" of the DWIparameters window?

2. How should I arrange my files in the folder I have to specify in the same
window? What I understood, from what I read in the manual, was that I had to
create three different folders, one for each non-zero b-value and to include
all the b0 slices in each of these folders.

3. If I do fiber tracking, how can I visualize the fibers?

Thank you very much and best regards,

Carolina Arboleda Clavijo
Research Assistant
Biomedical Imaging Center
Pontificia Universidad Cat?lica de Chile

2009/11/4 Huang, Shiliang <HuangS4 at uthscsa.edu>

> Hi everyone
> I use AIR to do register. But how can I guarantee using the registered data
> to calculate the tensor? Because the original data and the registered data
> are all exist. I do not know my results derived from the original data or
> registered data.
> Thanks
> Shiliang
>
> -----Original Message-----
> From: announcements-bounces at mristudio.org [mailto:
> announcements-bounces at mristudio.org] On Behalf Of xli at mristudio.org
> Sent: Wednesday, November 04, 2009 8:52 AM
> To: announcements at mristudio.org
> Subject: [Announcements] Tutorial in Kyoto Cancelled
>
> Dear MriStudio users,
>
> Due to unavailability of Dr. Mori, the tutorial in Kyoto, Japan on 11/14
> was
> cancelled. We sincerely apologize this change. Please contact us
> (xin_xu at mri.jhu.edu) if you have any question regarding this cancellation.
>
> Sincerely
>
>
> MriStudio Support
>
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-- 
Caro
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