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:
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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.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 _______________________________________________ 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.edu/ <https://secure-web.cisco.com/1mnjPXHDmORTo2qzofoDtbwzTCYp2Mry_QEuC1u53C9YhwuO5RtHHdvsCM-P27pJNuMlQNLoztWQHgd1hNXbja3M1m3d6jrP8z00z_amA8-0KsKZopuCBv5dYaezS2OMyrLD1IoC9oB1T8HfIGn69H7TJ-BeUqjP2uBgjTGlzxhVG8mLPbV8aoCXHnKrUXV_lk6gZeTxNcqYB1xk5XhqHNPTPnGq-RWlzAjtiTqh1qcDpbiPDK9J3sn6ssHgW7soQDRQ7-fL0QyEizKT4hgZGuYBQ9mezKMKEielWyWNLolhHemAWQ_rLaefaYBMlZGe5uxZe8rLxdJUmfHeD_ojWkQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> _______________________________________________ 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.edu/ <https://secure-web.cisco.com/1xCe-k0-FBbFPjOLCSjExZ15HPKKZ_O3ICGO2j-VWU0rJl543GCC-5i7SSG3KlSGwjyOmHNUAETErq5NNOdIC0B155tzhynK23zqk28yhorVaRiIR-dlkgiPmI3yQJ9Ha5n7M2ECyvgp1E_-y_Dikl9WnUvmLwZvVQXW6S96_uIqqgTdD3X_eG_Jue-vodE4bfCl6O34bvNWSeE23EXAeH19lDV61Pxojx25aD5O1PjXOfrvP4mkImXXKScTxjvHoE4MtQIffvguURsW4CTqLIbSjIBg9MGLyhiTX1onPHu62CMHRMv0QaQ1ZTzc9_fENtWO1wosrvJvmu-AzzM3_bg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F>
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