Hi all, I have been trying to take an SPM volume and extract FS thickness measurements.
I think I successfully took my spm volume from mni152 to fsaverage space (mni305) via the command line: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz --targ RTPJ_9mm_001_10_64_-54_16.img --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz Then I turned it into an ROI: mri_binarize --i $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min .0000000001 > From here I figured I could map it to the fsaverage surface (mri_vol2surf) > and extract thickness measurements (mri_segstats using > rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical thickness > workflow. However, some of my ROIs don't show up after I transform them. > From what I can tell, this is because they don't intersect with the fsaverage > surface. My thinking was that it might be better to stay within the individual subject space. So I would: 1. transform ROI to subject space 2. extract thickness values from rh.thickness However, I am struggling to get the roi into single subject space. I feel like this transform (or the inverse of it) should exist because I put all my subjects into fsaverage space via the -qcache flag, but i couldn't tell what to use. So I tried: fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $SUBJECTS_DIR/2506/fsaverage_to_indiv.dat But the registration doesn't look all that good. I am not sure if this is because the fsaverage is 'smoothed' or what. And then I am at a loss for how to put my roi into individual space and then extract thickness, or even if this is the right approach. Thanks, Stephanie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
