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while working on #408, we ran into minify issue where mri_convert was not found after minify-ing we verified mri_convert is working before minify-ing
mri_convert
commands used:
neurodocker generate docker \ --pkg-manager apt \ --base-image debian:buster-slim \ --freesurfer version=7.1.1 \ > freesurfer7.Dockerfile docker build --tag freesurfer:7.1.1 --file freesurfer7.Dockerfile .
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 ${PWD}/freesurfer_license.txt:/opt/freesurfer-7.1.1/license.txt \ -e FS_LICENSE="/opt/freesurfer-7.1.1/license.txt" \ freesurfer:7.1.1
neurodocker minify \ --container fs \ --dir /opt/freesurfer-7.1.1/ \ "$cmd1" "$cmd2"
The text was updated successfully, but these errors were encountered:
hi @sooyounga - does the file /opt/freesurfer-7.1.1/bin/mri_convert exist in the minified container?
/opt/freesurfer-7.1.1/bin/mri_convert
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while working on #408, we ran into minify issue where
mri_convert
was not found after minify-ingwe verified
mri_convert
is working before minify-ingcommands used:
The text was updated successfully, but these errors were encountered: