Docker: No third-party software embedding #3073
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With this change, "the MRtrix3 Docker container" will no longer embed within it third-party neuroimaging software commands. Any attempt to run an MRtrix3 script that depends on one of these tools will fail with a suitable error message.
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I have created the new repository and the first working version of the standalone container with alternative minification encoding: https://github.com/MRtrix3/mrtrix3-with3p/commits/dev/ |
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- Fix progress bar for when FSL FAST is not used for the cerebellum, and the FreeSurfer segmentations of the cerebellar hemispheres are propagated to the 5TT image. - New option -freesurfer_lut, for manually specifying the location of the FreeSurfer lookup table file; this permits utilisation of the script without environment variable FREESURFER_HOME being set, or indeed even the FreeSurfer software being present (related to #3073). - Add missing citations to help page documentation.
Lestropie
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- Fix progress bar for when FSL FAST is not used for the cerebellum, and the FreeSurfer segmentations of the cerebellar hemispheres are propagated to the 5TT image. - New option -freesurfer_lut, for manually specifying the location of the FreeSurfer lookup table file; this permits utilisation of the script without environment variable FREESURFER_HOME being set, or indeed even the FreeSurfer software being present (related to #3073). - Add missing citations to help page documentation.
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Conflicts: Dockerfile docs/installation/using_containers.rst python/mrtrix3/app.py
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clang-tidy review says "All clean, LGTM! 👍" |
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Closes #2601.
Closes #2736.
Working toward desired long-term solution for software containerisation.
The goal here is that "the MRtrix3 container" will not contain any third-party neuroimaging software tools. What will therefore happen following this PR, if one executes within this container an MRtrix3 Python command that attempts to execute such a third-party command, that MRtrix3 command will error out, with a suitable error message explaining the situation.
In conjunction with this, I aim to create a new repository within the MRtrix3 organisation, which provides the requisite data to construct a container that encapsulates both MRtrix3 and the set of third-party neuroimaging software commands that may be invoked by MRtrix3 Python commands. However that container will be explicitly labelled as having additional contents over and above just MRtrix3 (ideas for suitable naming welcome; "MRtrix3 and friends"? 🙃).
Make corresponding changes to
SingularityI've been having trouble doing Apptainer builds for some reason, so haven't finished the requisite work there.
Create new page in documentation explaining the dependence of some MRtrix3 commands on third-party tools, why those are unavailable in the official "core" "exclusively MRtrix3" container, and what options are available to users
Create new repository for container that includes third-party commands
(I already have some progress on this)