External Email - Use Caution
Hi Doug
I want to confirm that the signal any region flagged as cortex is restricted to
gray matter. If that is the case, then I finally have what I need. 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
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: Friday, February 25, 2022 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
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><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: Tuesday, February 22, 2022 at 3:00 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
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<mailto: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<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
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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