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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