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.
On 2/21/2022 12:57 PM, Jennifer Bramen wrote:
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://secure-web.cisco.com/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu2cTqbID6R2Q-DwaPaMHuhE_4IcMArFhh63A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
