Dear Doug,

Sorry - I'm probably missing something, as trying to write what u suggested (see below email history) didn't work (not sure what am I doing wrong).

I'm copying here what I did to get the average FA value to each region. Can u PLEASE write what do I need to change in order to get the MD value instead for the FA value, but keep the same format of the output ?

Thanks, I really appreciate the help !!

dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I160.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec

mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \
            --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz \
            --inv --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \
            --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg

mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/lowb.nii \
            --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg.mgz \
            --inv --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/mri/aparc+aseg2diff.mgz \
            --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat --no-save-reg

mri_mask /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii \
         /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz \
         /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz

mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa-masked

Message: 26
Date: Tue, 04 Feb 2014 11:10:25 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean diffusivity
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <52F110F1.5050007@nmr.mgh.harvard.edu>
Content-Type: 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 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
> Ben Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
>
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