Re: [Freesurfer] recon-all failed with FreeSurfer v8.0.0 (beta) on Mac

External Email - Use Caution  The fix for the error you posted when running the 8.0.0 beta release - which has to do with how some python code is run - will be fixed in the forthcoming 8.0.0 release; it’s unrelated to your environment setup. The commands that run the recon-all pi

[Freesurfer] Compute Cortical Thickness for grouped ROIs

External Email - Use Caution Hello, I am working on obtaining cortical thickness values for customized groups of ROIs. Currently, I extract thickness values for the standard set of ROIs using the following command: aparcstats2table --subjects [SUBJECT_ID] --hemi lh --meas t

[Freesurfer] Vertex Correspondences in Icosahedral Mesh Downsampling

External Email - Use Caution Hello, I am working on generating a vertex mapping file that identifies corresponding vertices across different levels of an icosahedral mesh. Specifically, for ico6, I want to determine which vertices contribute to each vertex in ico5 when downsampl

Re: [Freesurfer] Regarding Freesurfer for Ubuntu 24.01

External Email - Use Caution  We are aware that changes to the system libraries in Ubuntu 24 prevent installing packages that installed and ran fine in Ubuntu 22.  We hope to have a development build available for Ubuntu 24 in the near future.    Ubuntu 22.04 LTS was made genera

Re: [Freesurfer] mri_TumorSynth: command not found

External Email - Use Caution  I think that command is no longer/not supported and its wiki page is out of date; it has not been in any 7.X or 8.X  freesurfer distribution dating back to at least 2020. - R.On Feb 5, 2025, at 12:40, Zapaishchykova, Anna

[Freesurfer] Fw: mri_TumorSynth: command not found

Hi, Hope this email finds you well. Just wanted to report that https://surfer.nmr.mgh.harvard.edu/fswiki/TumorSynth package gets "mri_TumorSynth: command not found" on freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc and on 7.4 Best, Anna

Re: [Freesurfer] FreeSurfer coordinates

The coordinates reported in .label are in Freesurfer tkregister RAS space. You can use mri_label2label to map them to MNI 305 space https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yang Yifan Sent: Wednesday, February 5

[Freesurfer] FreeSurfer coordinates

External Email - Use Caution Hi FreeSurfer Developers, I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At t