Hi Stephanie, in your mri_vol2surf cmd, try using --projfrac-max -.2 1.2 .1 This will search for the max along the vector normal to the surface 20% below the white matter and 20% beyond the pial. doug
On 03/27/2013 04:42 PM, McMains, Stephanie wrote: > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
