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:
- transform ROI to subject space
- 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
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