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