External Email - Use Caution
Hi folks,
In the freesurfer/freesurfer:8.2.0 image from Dockerhub, straightforward `recon-all -all ...` runs have:
env: 'python3': No such file or directory
in STDERR. I'm running on a HTCondor cluster so I'm getting STDERR and STDOUT in separate files and can't see where this is exactly. It's the first line output to STDERR, followed by a bunch of
INFO: using NIfTI-1 sform (sform_code=1) threshold mask volume at 0.001 ...
that looks normal.
When I converted the Dockerfile to a singularity conf and created my own rockylinux:9 8.2.0 container, I didn't see this issue.
I've confirmed that going into the container in writable mode and running `yum install python3` fixes it.
(As a side note, recent updates being released as in-place patches with the same version number [instead of using minor version changes] is a bit confusing in places like dockerhub. I'm sure you all have a reason for doing it this way, but there are disadvantages too.)
Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging
Thanks for reporting this, Dan.
I've built a new container with python 3 and am pushing it to freesurfer/freesurfer:8.2.0 now.
-Paul
________________________________________ From: Dan Fitch dfitch@wisc.edu Sent: Friday, April 24, 2026 12:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Dockerhub image missing python3
External Email - Use Caution
Hi folks,
In the freesurfer/freesurfer:8.2.0 image from Dockerhub, straightforward `recon-all -all ...` runs have:
env: 'python3': No such file or directory
in STDERR. I'm running on a HTCondor cluster so I'm getting STDERR and STDOUT in separate files and can't see where this is exactly. It's the first line output to STDERR, followed by a bunch of
INFO: using NIfTI-1 sform (sform_code=1) threshold mask volume at 0.001 ...
that looks normal.
When I converted the Dockerfile to a singularity conf and created my own rockylinux:9 8.2.0 container, I didn't see this issue.
I've confirmed that going into the container in writable mode and running `yum install python3` fixes it.
(As a side note, recent updates being released as in-place patches with the same version number [instead of using minor version changes] is a bit confusing in places like dockerhub. I'm sure you all have a reason for doing it this way, but there are disadvantages too.)
Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
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Dan Fitch -
Wighton, Paul