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.

 

 

 

 

 

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

        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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