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Hello Adam,

Sorry for the delay in getting back to you.

If possible, I would do “sudo apt install ./freesurfer_ubuntu22-8.0.0-beta_amd64.deb” so that you end up with FREESURFER_HOME=/usr/local/freesurfer/8..0.0-beta and so that the linux install tools will have installed any missing packages on your system. Then try putting SUBJECTS_DIR to be under a non-system subdirectory, e.g., “mkdir $HOME/subjects” and then “export SUBJECTS_DIR=$HOME/subjects”. The recon-all command should be run with normal user (non-root, non-sudo) privileges.

- R.

On Nov 6, 2024, at 13:51, Raikes, Adam C - (adamraikes) <adamraikes@arizona.edu> wrote:

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Hello Developers,

I was attempting to test out the beta version of 8.0.0 and I recognize that this is on-going development. I installed it in a Singularity image running Ubuntu 22.04. Getting recon-all to run at all requires setting an environmental variable (FS_ALLOW_DEEP=1), which I did and recon-all launches. However, it crashes very quickly. In short, orig/001.mgz is created and then it immediately attempts to run mri_synthstrip on orig.mgz, which does not exist yet. See attached logs.

Adam C. Raikes, PhD

Imaging Projects Manager

Center for Innovation in Brain Science

University of Arizona

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