RE:
selection of mgx instead of gtm: I am analyzing
amyloid PET data and I believe it is recommended to
extract gray matter localized PET data. Is that what
I am doing by using the mgx image?
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
You
need to first map your pet to the anatomical space
using mri_vol2vol and the registration
glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the
mgx data instead of using the output from the gtm?
Note that you cannot use the white matter values
that come from mgx.
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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
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:
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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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