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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.edumailto: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.edumailto: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.edumailto: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.edumailto: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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