PetSurfer surface-based SUVR

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Re: Ubuntu 24 release

Mia Anthony

6 Jun 2025 6 Jun '25

8:19 p.m.

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Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

mris_fwhm --smooth-only --i all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi lh mris_fwhm --smooth-only --i all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi rh

Do I need to run the mri_glmfit command? For example: mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage lh --fsgd g1v0.fsgd mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage rh --fsgd g1v0.fsgd

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you, Mia

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Mia Anthony

10 Jun 10 Jun

1:40 p.m.

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Hello,

I am a following up on my prior question. Thank you

Mia

From: Mia Anthony manthon6@stanford.edu Date: Friday, June 6, 2025 at 8:19 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: PetSurfer surface-based SUVR Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you, Mia

Douglas N. Greve

11 Jun 11 Jun

4 p.m.

That is all you need to run!

On 6/6/2025 8:19 PM, Mia Anthony wrote:

...

External Email - Use Caution

Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

mris_fwhm --smooth-only --i all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi lh

mris_fwhm --smooth-only --i all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage --hemi rh

Do I need to run the mri_glmfit command? For example:

mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage lh --fsgd g1v0.fsgd

mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface fsaverage rh --fsgd g1v0.fsgd

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you,

Mia

Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...

Mia Anthony

17 Jun 17 Jun

1:25 p.m.

External Email - Use Caution

Just to clarify: mris_fwhm or mri_glmfit is the last command I need to run? Can I extract SUVR values from all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?

Thank you

From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Wednesday, June 11, 2025 at 4:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: PetSurfer surface-based SUVR That is all you need to run! On 6/6/2025 8:19 PM, Mia Anthony wrote:

External Email - Use Caution Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you, Mia

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Douglas N. Greve

19 Jun 19 Jun

12:37 p.m.

What do you mean by extract here? What do you want? A map of SUVR? A group map or the individual maps? Or do you want ROI averages? If so for the group or individually?

On 6/17/2025 1:25 PM, Mia Anthony wrote:

...

External Email - Use Caution

Just to clarify: mris_fwhm or mri_glmfit is the last command I need to run? Can I extract SUVR values from all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?

Thank you

*From: *Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Wednesday, June 11, 2025 at 4:01 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: PetSurfer surface-based SUVR

That is all you need to run!

On 6/6/2025 8:19 PM, Mia Anthony wrote:

*        External Email - Use Caution *

Hello FS,

I have calculated regional SUVR and would like to calculate SUVR
on the surface. I have followed the wiki tutorial, including PVC,
through smoothing on the surface. The last commands I ran are:

mris_fwhm --smooth-only --i all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz
--fwhm 5 --o all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s
fsaverage --hemi lh

mris_fwhm --smooth-only --i all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz
--fwhm 5 --o all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s
fsaverage --hemi rh

Do I need to run the mri_glmfit command? For example:

mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface
fsaverage lh --fsgd g1v0.fsgd

mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --surface
fsaverage rh --fsgd g1v0.fsgd

Will the mri_glmfit output provide surface-based SUVR, or will I
need to run additional commands after?

Thank you,

Mia



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Mia Anthony

24 Jun 24 Jun

1:14 p.m.

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I would like to get a tac file of the ROI averages at the surface for each subject.

From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Thursday, June 19, 2025 at 12:38 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: PetSurfer surface-based SUVR What do you mean by extract here? What do you want? A map of SUVR? A group map or the individual maps? Or do you want ROI averages? If so for the group or individually? On 6/17/2025 1:25 PM, Mia Anthony wrote:

External Email - Use Caution Just to clarify: mris_fwhm or mri_glmfit is the last command I need to run? Can I extract SUVR values from all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?

Thank you

From: Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Date: Wednesday, June 11, 2025 at 4:01 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: PetSurfer surface-based SUVR That is all you need to run! On 6/6/2025 8:19 PM, Mia Anthony wrote:

External Email - Use Caution Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you, Mia

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Douglas N. Greve

27 Jun 27 Jun

11:11 a.m.

If you just want the TAC for an ROI, you can use mri_gtmpvc. If you are not actually doing any PVC, then you can use mri_segstats (but you have to resample to the anatomical space)

On 6/24/2025 1:14 PM, Mia Anthony wrote:

...

External Email - Use Caution

I would like to get a tac file of the ROI averages at the surface for each subject.

*From: *Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Thursday, June 19, 2025 at 12:38 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: PetSurfer surface-based SUVR

What do you mean by extract here? What do you want? A map of SUVR? A group map or the individual maps? Or do you want ROI averages? If so for the group or individually?

On 6/17/2025 1:25 PM, Mia Anthony wrote:

*        External Email - Use Caution *

Just to clarify: mris_fwhm or mri_glmfit is the last command I
need to run? Can I extract SUVR values from
all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?

Thank you

*From: *Douglas N. Greve <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Date: *Wednesday, June 11, 2025 at 4:01 PM
*To: *freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] Re: PetSurfer surface-based SUVR

That is all you need to run!

On 6/6/2025 8:19 PM, Mia Anthony wrote:

    *        External Email - Use Caution *

    Hello FS,

    I have calculated regional SUVR and would like to calculate
    SUVR on the surface. I have followed the wiki tutorial,
    including PVC, through smoothing on the surface. The last
    commands I ran are:

    mris_fwhm --smooth-only --i
    all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o
    all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage
    --hemi lh

    mris_fwhm --smooth-only --i
    all.rh.mgx.ctxgm.fsaverage.sm00.nii.gz --fwhm 5 --o
    all.rh.mgx.ctxgm.fsaverage.sm05.nii.gz --cortex --s fsaverage
    --hemi rh

    Do I need to run the mri_glmfit command? For example:

    mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz
    --surface fsaverage lh --fsgd g1v0.fsgd

    mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz
    --surface fsaverage rh --fsgd g1v0.fsgd

    Will the mri_glmfit output provide surface-based SUVR, or will
    I need to run additional commands after?

    Thank you,

    Mia

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Mia Anthony

7 Jul 7 Jul

10:07 p.m.

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What if I want the TAC for a custom cortical atlas, such as Yeo 7?

I have the Yeo 7 annot files and tried running gtmseg with this command: gtmseg --s sub-"$subject" --ctx-annot Yeo2011_7Networks_N1000 lhbase rhbase --xcerseg --o gtmseg+Yeo2011_7Networks.mgz

Since I am only interested in the cortical SUVR, I was thinking that the default subcortical segmentation would be fine, but I received the error below, and I’m not sure how to interpet it. Thanks for your help.

------------------- xcerebralseg Done mri_gtmseg --s sub-0141 --usf 2 --o gtmseg+Yeo2011_7Networks.mgz --apas apas+head.mgz --ctx-annot Yeo2011_7Networks_N1000.annot lhbase rhbase --no-subseg-wm --no-keep-cc --no-keep-hypo

7.4.1 cwd /gpfs/fs2/scratch/tbaran2_lab/manthon6/petsurfer cmdline mri_gtmseg --s sub-0141 --usf 2 --o gtmseg+Yeo2011_7Networks.mgz --apas apas+head.mgz --ctx-annot Yeo2011_7Networks_N1000.annot lhbase rhbase --no-subseg-wm --no-keep-cc --no-keep-hypo sysname Linux hostname bhp0008.bluehive.circ.private machine x86_64 user manthon6 subject sub-0141 USF 2 OutputUSF 2 apasfile apas+head.mgz wmannotfile NULL ctxannotfile Yeo2011_7Networks_N1000.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 0 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 mri_gtmseg supposed to be reproducible but seed not set Entering TissueTypeSchemaDefaultHead() schema default-apr-2019+head master tissue type schema default-apr-2019+head Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading /scratch/tbaran2_lab/manthon6/petsurfer/t1_freesurfer/ses-01/sub-0141/mri/apas+head.mgz Loading surfaces t = 2.4062 Loading annotations t = 4.7385 error: No such file or directory Not segmenting WM error: # elements (163842) in /scratch/tbaran2_lab/manthon6/petsurfer/t1_freesurfer/ses-01/sub-0141/label/lh.Yeo2011_7Networks_N1000.annot and # vertices (122809) don't match ERROR: mri_gtmseg --s sub-0141 --usf 2 --o gtmseg+Yeo2011_7Networks.mgz --apas apas+head.mgz --ctx-annot Yeo2011_7Networks_N1000.annot lhbase rhbase --no-subseg-wm --no-keep-cc --no-keep-hypo gtmseg exited with errors

From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Friday, June 27, 2025 at 11:11 AM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: PetSurfer surface-based SUVR If you just want the TAC for an ROI, you can use mri_gtmpvc. If you are not actually doing any PVC, then you can use mri_segstats (but you have to resample to the anatomical space) On 6/24/2025 1:14 PM, Mia Anthony wrote:

External Email - Use Caution I would like to get a tac file of the ROI averages at the surface for each subject.

From: Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu Date: Thursday, June 19, 2025 at 12:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: PetSurfer surface-based SUVR What do you mean by extract here? What do you want? A map of SUVR? A group map or the individual maps? Or do you want ROI averages? If so for the group or individually? On 6/17/2025 1:25 PM, Mia Anthony wrote:

External Email - Use Caution Just to clarify: mris_fwhm or mri_glmfit is the last command I need to run? Can I extract SUVR values from all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?

Thank you

External Email - Use Caution Hello FS,

I have calculated regional SUVR and would like to calculate SUVR on the surface. I have followed the wiki tutorial, including PVC, through smoothing on the surface. The last commands I ran are:

Will the mri_glmfit output provide surface-based SUVR, or will I need to run additional commands after?

Thank you, Mia

_______________________________________________

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Douglas N. Greve
Mia Anthony