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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Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

2014-02-04 5:45 GMT+02:00 Rotem Saar saar.rotem@gmail.com:

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

Hello all,

I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and latter. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10% variation in intensity at any given voxel between versions. I've been comparing the mean_f1 images by subtracting the new - old using fslmaths. Has anyone else seen this?

Thanks, Jeff