The Dockerfile is missing installation of dwidenoise from Mrtrix3 to run the dwi workflow #1175
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https://www.mrtrix.org/download/linux-anaconda/ Install
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Installing on its own has a lot of dependenciesThat's a lot of potential conflicts. We could do a build stage where we install and then copy, but maybe instead it makes sense to copy from their docker image: https://hub.docker.com/r/mrtrix3/mrtrix3/tags |
oesteban
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Mar 18, 2024
Update the docker build procedure to leverage multi-stage builds and lay the ground for nipreps#1175.
oesteban
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Mar 19, 2024
Implements [@effigies' solution](#1175 (comment)) leveraging Docker multi-staged builds. Checked linked libraries within the Docker container: ``` $ ldd /usr/local/bin/dwidenoise linux-vdso.so.1 (0x00007fff6db65000) libmrtrix.so => /usr/local/bin/../lib/libmrtrix.so (0x00007f4e2b757000) libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f4e2b574000) libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f4e2b48d000) libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f4e2b472000) libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4e2b46d000) libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f4e2b242000) /lib64/ld-linux-x86-64.so.2 (0x00007f4e2bac2000) libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f4e2b227000) libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f4e2b19f000) libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f4e2b162000) librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f4e2b15d000) libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f4e2b0bb000) libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f4e2afa7000) liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f4e2af7e000) libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f4e2af6d000) libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f4e2ae87000) libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f4e2ae71000) libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f4e2ae65000) ldd /usr/local/lib/libmrtrix.so linux-vdso.so.1 (0x00007ffc0a0b6000) libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f431b203000) libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f431b17b000) libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f431b13e000) libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f431af5b000) libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f431ae74000) libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f431ae57000) libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f431ae52000) libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f431ac29000) /lib64/ld-linux-x86-64.so.2 (0x00007f431b4d5000) libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f431ab89000) libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f431aa75000) liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f431aa4c000) libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f431aa39000) libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f431a953000) libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f431a93d000) librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f431a938000) libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f431a92e000) ``` And also tested *MRIQC* locally on DWI data. Resolves: #1175.
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What happened?
I built the singularity image from the Dockerfile as it currently is in nipreps/mriqc:master and tried to run it on our dense-sampling dataset containing DWI images.
But that image is missing the installation of
dwidenoiseto run the dwi workflow of MRIQC.dwidenoise is a package from mrtrix3.
The Dockerfile thus needs to be adapted to include this package.
What command did you use?
What version of the software are you running?
nipreps/mriqc:master
How are you running this software?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
No response
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