[Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, M

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, M

[Freesurfer] Freesurfer v8.0.0 error

External Email - Use Caution Hello FreeSurfer Developers, I installed freesurfer 8.0.0 successfully but failed to run "recon-all -i *** -s *** -all -localGI -qcache" for any subjects. I tried this version 8.0.0beta on both macos latest version and ubuntu 22.04, the error was the s

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

There have been some updates to recon-all-clinical for 7.4.1 - see the instruction here https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical The updated version also uses colortable_BA_thresh.txt, which you need to download from https://github.com/freesurfer/freesurfer/blob/dev/distribu

Re: [Freesurfer] recon-all-clinical rh.BA_exvivio.annot error

The downloaded colortable_BA_thresh.txt needs to be place in $FREESURFER_HOME/average/. From: Huang, Yujing Sent: Wednesday, December 11, 2024 12:05 PM To: Freesurfer support list Cc: Benjamin Billot ; Iglesias Gonzalez, Juan E. Subject: RE: recon-all-clinical rh.BA_exvivio.annot error There

Re: [Freesurfer] Freesurfer v8.0.0 error

Can you add those options as shown in the output '-fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph'? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ??? Sent: Wednesday, December 11, 2024 11:53 AM To: freesurfer@nmr.mgh.harv

Re: [Freesurfer] Fwd: LME matrix design

External Email - Use Caution Hi Daniel, please find my responses below. Hope this helps, Kersten External Email - Use Caution Hello FreeSurfer experts, I am currently working through the linear mixed effects pipeline to assess longitudinal cortical thickness changes

[Freesurfer] needed: tools to work with synthmorph deformations in ANTS and FSL pipelines.

External Email - Use Caution mri_synthmorph is simply an amazing SOTA tool that I want to incorporate into all my pipelines. However, I am unsure how to convert the combined affine+nonlinear deformation image into a format that can be worked with by ants or FSL. Optimally, synthmo