I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:
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If I only want to extract intensity from gray matter, do I need to add
an additional mask?
Thanks!
Jennifer
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------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
The GTM gives you values for each ROI regardless of whether it is GM,
WM, or CSF. They will probably give you similar answers, but the GTM
will be more robust.
On 2/21/2022 8:48 PM, Jennifer Bramen wrote:
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Thanks! Yes, I already mapped my PET to anatomical space using
mri_vol2vol and glmdir/aux/bbpet2anat.lta.
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
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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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