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 with the FA value for each ROI (for each subject).
I wrote my FA script, and asked u to advise on how to convert it to my needs (MD instead of FA), u wrote -

> 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

(steps below for FA values ended fine) - this is what I did -

1)  dt_recon --i /usr/local/freesurfer/
  subjects/Anatomy0981/DTI/I160.dcm
  --s Anatomy0981 --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec

2) mri_vol2vol --mov
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
             --targ
  /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz \
             --inv --interp nearest --o
  /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz \
             --reg
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg

3) mri_label2vol --mov
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
             --targ
  /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz \
             --inv --interp nearest --o
  /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg2diff.mgz \
             --reg
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg

4) mri_segstats --seg-erode 1
  /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab
  $FREESURFER_HOME/FreeSurferColorLUT.txt --i
  /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum
  /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked

error after step 3: ERROR: Option --mov unknown
Trying to use vol2vol instead of label2vol ended successfully, but then when trying to perform step 4, it failed again -
ERROR: Option /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