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.
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
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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