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Alright. I'll give it a shot and let you know.
Adam Raikes, PhD, ATC
Assistant Scientific Investigator
Center for Innovation in Brain Science
University of Arizona
________________________________
From: fsbuild <fsbu...@contbay.com>
Sent: Monday, November 18, 2024 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXT] Re: [Freesurfer] Synthstrip error in FS v. 8.0.0 beta
External Email
________________________________
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)
<adamrai...@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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