Are you doing an ROI analysis or a voxel-wise analysis? If an ROI
analysis, then use mri_gtmpvc (with or without PVC). This will give you
GM, WM, and CSF ROIs. Or do you mean you want a single average across
all GM?
On 2/24/2022 1:15 PM, Jennifer Bramen wrote:
External Email - Use Caution
I would like to measure uptake exclusively in gray matter. What would
you recommend to accomplish this?
In my previous message, I was wondering if adding a gray matter mask
would be a potential way to restrict the analysis to gray matter. Thanks!
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: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:
* External Email - Use Caution *
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>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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:
* External Email - Use Caution *
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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