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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: External Email - Use Caution 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, PhDImaging Projects ManagerCenter for Innovation in Brain ScienceUniversity of Arizona <recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 fsbuild@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
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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:
External Email - Use Caution
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
<recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/12UGdmfVJG3NbNBW2m2HH04DsbkwElbeaKAYD8nAbdImyR4...https://secure-web.cisco.com/12UGdmfVJG3NbNBW2m2HH04DsbkwElbeaKAYD8nAbdImyR45TWojSKR3hGsOkDNvtc4Eb530XvwJtU4NZsK_EJnKJZIRjPwAzkBB9cZ1xCyN1-eMEtyxvC_yro54-Rs76dzaoCpzZkXYt-8AfoqO2_ZVuQojK8_T9sn__JvlI7MIRwXDPTj0Fvcc79RJUdIlReZucJJKdbp3JAv9RUMsm0n96pG9mHUPN4fp9xSEH-Af8_ptlkkI9iZIzC17e3hHztovUlggXZpBlZfd8O22Trx1FPxed_vLn9ddMNDh8flQ_pvuYWyM09ut06XMjB5rMEeoR-pGkKq4ayRycZVFu8Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
freesurfer@nmr.mgh.harvard.edu
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fsbuild -
Raikes, Adam C - (adamraikes)