Re: [External] Re: recon-all fails with "Invalid FreeSurfer license key" when executed via Docker SDK but works interactively
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I use the interactive option, e.g., $ docker run -dit —name <container name> <image name> Everything in the environment works, including using FS_LICENSE with newer versions of freesurfer to find the license file. - R.
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Hello!
After trying the different commands to inspect the license.txt file I did not find anything strange. I printed the environment variables at runtime showing this: environ({'HOSTNAME': '42c5cd6166c9', 'PYTHON_VERSION': '3.11', 'LANGUAGE': 'en_US.UTF-8', 'FREESURFER_SETUP': '/usr/local/freesurfer/SetUpFreeSurfer.sh', 'MINC_BIN_DIR': '/usr/local/freesurfer/mni/bin', 'GOOGLE_APPLICATION_CREDENTIALS': '/run/secrets/my_secret_id', 'PIP_CONFIG_FILE': '/pip.conf', 'HOME': '/root', 'LANG': 'en_US.UTF-8', 'MNI_DIR': '/usr/local/freesurfer/mni', 'PERL5LIB': '/usr/local/freesurfer/mni/lib/perl5/5.8.0', 'FREESURFER_HOME': '/usr/local/freesurfer', 'TERM': 'xterm', 'SHLVL': '0', 'SUBJECTS_DIR': '/usr/local/freesurfer/subjects', 'LD_LIBRARY_PATH': 'usr/local/freesurfer/lib:/usr/local/freesurfer/mni/lib:/usr/local/freesurfer/mni/lib64:', 'FS_LICENSE': '/usr/local/freesurfer/license.txt', 'LC_ALL': 'en_US.UTF-8', 'PATH': '/usr/local/freesurfer/bin:/usr/local/freesurfer/mni/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'GIT_PYTHON_REFRESH': '0'})
I run the command mri_convert inside the docker after replacing the license.txt with different licenses we have available but all of them failed.
root@4f8634b3d867:/usr/local/freesurfer# *echo *$FS_LICENSE /usr/local/freesurfer/license.txt
root@4f8634b3d867:/usr/local/freesurfer# *mri_convert */root/INPUT/DATA/input_t1/mprage_noface.nii.gz /root/OUTPUT/FREESURFER/mri/orig/001.mgz mri_convert /root/INPUT/DATA/input_t1/mprage_noface.nii.gz /root/OUTPUT/FREESURFER/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /root/INPUT/DATA/input_t1/mprage_noface.nii.gz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1ZHYDvB9d9O9fKCTvNFG2y9kXnG3M1CZuHSZgNdj_-fO0W1q... to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. --------------------------------------------------------------------------
I fail to see the solution to this matter, the license is working in other dockers we have for higher versions of FreeSurfer, might be that the license can expire? We think we have a proper license to use for version 5.3.0 but would it be possible to ask for another one?
Thank you all for your support,
On Thu, 16 Oct 2025 at 22:47, fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionI use the interactive option, e.g.,
$ docker run -dit —name <container name> <image name>
Everything in the environment works, including using FS_LICENSE with newer versions of freesurfer to find the license file.
- R.
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Óscar Peña-Nogales