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-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@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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