Minimise freesurfer 7.1.1 - nu_correct not found

[jakepalmer]

Freesurfer's nu_correct command isn't found when calling mri_nu_correct.mni while using neurodocker-minify. When mri_nu_correct.mni is called from inside the docker container without the minify command it completes without error. I've read a few other issues that relate to problems with perl (e.g. mentioned in #321 and #333).

Command to build:

docker run --rm repronim/neurodocker:master generate docker \
        --base=nvidia/cuda:9.1-base-ubuntu16.04 \
        --pkg-manager=apt \
        --freesurfer version=7.1.1 | docker build -t fs:test -

Then assuming license.txt and T1.nii.gz exist in $PWD:

cmd1="mri_convert /home/T1.nii.gz /home/T1.mgz"
cmd2="mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2"

docker run --rm -itd \
    --name fs \
    --security-opt=seccomp:unconfined \
    -v ${PWD}:/home \
    -v ${PWD}/license.txt:/opt/freesurfer-7.1.1/license.txt \
    -e FS_LICENSE="/opt/freesurfer-7.1.1/license.txt" \
    fs:test

neurodocker-minify \
    --container fs \
    --dirs-to-prune /opt/freesurfer-7.1.1/ \
    --commands "$cmd1" "$cmd2"

Full output printed to terminal is in this text file, but important part seems to be:

[NEURODOCKER 2021-06-24 23:26:56,594 INFO]: /opt/freesurfer-7.1.1/bin/mri_nu_correct.mni
[NEURODOCKER 2021-06-24 23:26:56,621 INFO]: --i /home/T1.mgz --o /home/T1_N3.mgz --n 2
[NEURODOCKER 2021-06-24 23:26:56,674 INFO]: nIters 2
[NEURODOCKER 2021-06-24 23:26:56,732 INFO]: mri_nu_correct.mni 7.1.1
[NEURODOCKER 2021-06-24 23:26:56,782 INFO]: Linux f7a075905ebd 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
[NEURODOCKER 2021-06-24 23:26:56,843 INFO]: Thu Jun 24 13:26:56 UTC 2021
[NEURODOCKER 2021-06-24 23:26:57,065 INFO]: tmpdir is /home/tmp.mri_nu_correct.mni.114
[NEURODOCKER 2021-06-24 23:26:57,091 INFO]: nu_correct: Command not found.
[NEURODOCKER 2021-06-24 23:26:57,184 INFO]: /
[NEURODOCKER 2021-06-24 23:26:57,214 INFO]: mri_convert /home/T1.mgz /home/tmp.mri_nu_correct.mni.114/nu0.mnc -odt float
[NEURODOCKER 2021-06-24 23:26:57,363 INFO]: mri_convert /home/T1.mgz /home/tmp.mri_nu_correct.mni.114/nu0.mnc -odt float
[NEURODOCKER 2021-06-24 23:27:37,296 INFO]: reading from /home/T1.mgz...

minify.txt

Thanks for your help!

[sooyounga]

we didn't have the same issue when minify-ing, we ran into mri_convert issue however.
there's a new command for minify using neurodocker minify instead of neurodocker-minify:

neurodocker minify \
    --container fs \
    --dir /opt/freesurfer-7.1.1/ \
    "$cmd1" "$cmd2"

we used the base image as demian using this command:

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:buster-slim \
    --freesurfer version=7.1.1 \
> freesurfer7.Dockerfile

since minify-cation was not proper, do you want to try this again using the base image we used and with the new command? the minify doesn't work as expected so we'll open a new issue

[djarecka]

since we were not able to reproduce and there is no new comments, we will close it for now. feel free to reopen