Re: [Freesurfer] mris_register external atlas

External Email - Use Caution Thank you, that worked! To recap, I've been trying to align the annotation files from the UNC cortical surface atlas to my subjects. I'm using Freesurfer version 8.0.0 with Linux. Following mri_surf2surf with my registration file, I got a new annotat

Re: [Freesurfer] mris_register external atlas

You should be able to use mri_annotation2label to extract all the labels in the annot as separate label files Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stefanie Bradley Sent: Wednesday, April 2, 2025 3:15 PM To: Zollei, Lilla,Ph.D. ; Freesurfer support list Subje

Re: [Freesurfer] mris_register external atlas

External Email - Use Caution Hi Bruce, Thanks. Should I be doing this step before or after mri_surf2surf? (on the external atlas .annot or the newly registered .annot)? Thanks, Stef From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fi

Re: [Freesurfer] Freesurfer Question - Pediatric pathology

Hi Stefanie, We have an in-house preschooler version of the script and for 4.5 / 5 yr-olds (depending on your data quality) you could also try to use the regular pipeline. We also wrote up a manual QC / editing guideline for 4-6 year-olds that you might want to look at: https://surfer.nmr.mgh.ha

Re: [Freesurfer] mris_register external atlas

Hi Stef I would do it at the end on whichever annot you want to convert into labels Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stefanie Bradley Sent: Wednesday, April 2, 2025 3:29 PM To: Freesurfer support list ; Zollei, Lilla,Ph.D. Subject: Re: [Freesurfer] mris_

Re: [Freesurfer] mris_register external atlas

External Email - Use Caution Hi Bruce, Thanks. The command seems to stall when I try to run it following mri_surf2surf. It ends like this: "calling annotation2labelV2() ..." And then doesn't create any labels. Not sure if this is a bug? Stef Fr

Re: [Freesurfer] Importing surface meshes from 3rd party cortical surface reconstruction tools for analysis in fsaverage template space

Hi Jim, I am sorry I missed your message. Are your questions still relevant? Apologies, Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of James Hengenius Sent: Friday, December 13, 2024 2:49 PM To: Freesurfer support list Subject: [Freesurfer] Imp

[Freesurfer] cvs register error

External Email - Use Caution Dear all, I am attempting to use my own data and follow the instructions on the petsurfer wiki. I ran the following command: `mri_cvs_register --mov 001 --template cvs_avg35_inMNI152` The output showed: [...] `mri_cvs_register: Step 1 (spherical reg