I just sent info on how to do this, but see step 5 in the wiki
On 2/14/2022 6:27 PM, Jennifer Bramen wrote:
External Email - Use Caution
Dear Freesurfer Developers
I am doing an ROI--based amyloid PET scan analysis. I am following the
steps from the PetSurfer wiki. I see instructions for how to do a
cortical surface-based group analysis. I also see how to do a
subcortical ROI-based analysis. However, I cannot find detailed
instructions for performing a cortical ROI-based analysis.
This is how I think I should adapt the instructions from your
subcortical ROI-based analysis instructions for cortical gray matter:
mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg
$PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz
mri_fwhm --smooth-only --i
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz --fwhm 5 --o
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz
Can someone confirm or correct these commands? I am especially
concerned that I have selected the wrong mask.
Thanks you!
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
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