External Email - Use Caution
I am trying to extract mean intensity in my PET data for every ROI. Doug said to run mri_segstats passing the PET with --i and using --seg to spec the segmentation. I would like to confirm that I am using this properly.
mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg
where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data registered and resampled into the individual’s T1-weighrd MRI space.
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 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, February 16, 2022 at 7:30 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same thing just using the MNI305-based (2mm) segmentation On 2/14/2022 6:11 PM, Jennifer Bramen wrote:
External Email - Use Caution Dear Freesurfer Developers
I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the subcortical gray matter mask.
How do I extract mean intensity within all of the subcortical ROI?
Thank 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 1301 20th St. #150 Santa Monica, CA 90404 Phone: 310-525-0865 | Fax: 310-315-4069
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