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:

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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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