Hi Doug,
Can u help ?
Thanks
Rotem
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev
Beer-Sheva 84105
Israel
2014/1/6 Bruce Fischl
> it probably doesn't matter, but Doug is the Talairach expert, so perhaps
> he can comment
> Bruc
red, anterior-posterior are
green ect...
is this possible ?
Thanks
Rotem
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev
Beer-Sheva 84105
Israel
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear freesurfer experts,
Can u please advise on how to extract the mean diffusivity value for each
ROI from the wmparc file ?
I know how to extract the FA value, but interested in the MD value also for
the same regions.
Thanks
Rotem
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
: text/plain; charset=ISO-8859-1; format=flowed
Use mri_label2vol to transfer the wmparc.mgz into the DTI space, then
use mri_segstats with --seg-erode 1 to compute summaries of the MD in
each region
doug
On 02/03/2014 10:45 PM, Rotem Saar wrote:
> Dear freesurfer experts,
>
> Can u p
on
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz unknown
Can u advise on what am I doing wrong ?
Thanks !!
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev
Beer-Sheva 84105
Israel
___
p
Rotem
2014-03-17 8:42 GMT+02:00 Rotem Saar :
> Dear Doug,
>
> I'm now working with freesurfer 5.3, for this example, subject is
> "Anatomy0981". A while ago I wrote to the list trying to extract the MD
> values for each ROI as in the diffusion analysis that ends
really point to the
problem, thus asking for your help.
Attached is the table again,
Thanks
Rotem
> The values look about right in the table. Your pipeline looks ok,
> thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output
> of mri_vol2vol (fa_FOLDER-NAME.nii).
> d
really point to the
problem, thus asking for your help.
Attached is the table again,
Thanks
Rotem
> The values look about right in the table. Your pipeline looks ok,
> thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output
> of mri_vol2vol (fa_FOLDER-NAME.nii).
> d
step further towards understanding the problem and
its solution ?
Thanks for your time,
Rotem
On 04/07/2013 06:48 AM, Rotem Saar wrote:
> Hi Doug,
>
> Thanks for your answer.
> I changed the last step as u suggested, but I think I need to clarify
> my question:
> Indeed values
-1; format=flowed
>
> That is a good value, so the regis not the problem. If you upload your
> dt_recon folder as well as your recon-all folder for that subject I'll
> take a look.
> doug
>
> On 04/11/2013 10:02 AM, Rotem Saar wrote:
> > Hi Douge,
> >
> &
the axial views that you sent, the artifact
> that you're pointing to looks like misalignment between consecutive coronal
> slices, which could be due to head motion.
>
> a.y
>
>
> On Tue, 25 Jun 2013, Rotem Saar wrote:
>
> Dear Anastasia,
>>
>> I tried sev
Hi,
My name is Rotem, I'm a PhD. student and recently started to work with
freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION
For several weeks, I have been trying to operate a script for FA values,
with no success, and would really appreciate your help with shading some
li
Hi all,
I run into somthing that seems odd to me and wanted to consult -
I run the following script for getting the FA values from my DTI scans:
1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm
--s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
/usr/lo
and the anatomicals?
>
> cheers
> Bruce
>
>
>
> On Mon, 18 Feb 2013, Rotem Saar wrote:
>
> Hi all,
>>
>> I run into somthing that seems odd to me and wanted to consult -
>> I run the following script for getting the FA values from my DTI scans:
>>
&
2013/3/5 Rotem Saar
> Hi
>
> Attached is some pictures that might help ? Is this what you meant ?
> Looking at this again - something is weird but I can't say what...
> I can ZIP the data of one subject and send it to you but I don't feel
> comfortable asking
(maybe I missed it?)
If not - does manual ROI drawing and following,volume calculation is
possible using freesurfer?
Thanks !
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105
School of Social Work
Ashkelon Academic College
me of a specific ROI today using and advance freesurfer
version (5+) - Do I need to run recon-all again with the newer version?
Many thanks !
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105
School of Social Work
Ashkelon Aca
one that was created from the dicom header or the one
created for NIFTI format using MRIconvert ?
Thanks
Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105
School of Social Work
Ashkelon Academic College, Ashkelon, 78211
Israel
outh Euclid Ave. Tel: 314-747-6173
> St. Louis, MO ?63110 Email: mha...@wustl.edu
>
> From: Rotem Saar
> Reply-To: Freesurfer support list
> Date: Monday, July 21, 2014 1:54 PM
> To: "freesurfer@nmr.mgh.harvard.edu"
> Subject: [Freesurfer] Diffusion analysis q
Jul 2014, Rotem Saar wrote:
> Dear Anastasia & Michael,
>
> Thank u for your answers (I attached my last email and your answers at the
> end of this email.
>
> I still want to specify my question. If I only want to extract FA values
> using the following script (see script be
Jul 2014, Rotem Saar wrote:
> Dear Anastasia & Michael,
>
> Thank u for your answers (I attached my last email and your answers at the
> end of this email.
>
> I still want to specify my question. If I only want to extract FA values
> using the following script (see script be
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