amiklos/simnibs repository overview

Two different dockers, one with version numbers 1.x and the other is 3.2x. The former is designed to run the second half of simnibs from jupyter python, the 3.2x series (c is currently the good one) is to implement headreco here you have to call the docker in this way:
docker run --rm --network host -e MLM_LICENSE_FILE=27000@adrian -v /data/BIDS/sub-sucject01/ses-session01/anat:/anat -v /nethome/amiklos/work/ECT/simNIBS/mikitest:/home/matlab/output amiklos/simnibs:3.2c subject01 /anat/sub-subject01_ses-session01_run-01_T1w.nii.gz /anat/sub-subject01_ses-session01_run-01_T2w.nii.gz

where adrian is the machine where the matlab license server is (substitute your own), usually listening on 27000 port, also make --network host

Original call would be: headreco all subject01 /data/BIDS/sub-sucject01/ses-session01/anat/sub-subject01_ses-session01_run-01_T1w.nii.gz /data/BIDS/sub-sucject01/ses-session01/anat/sub-subject01_ses-session01_run-01_T2w.nii.gz

Dockerfile
FROM matlab:r2020a

MAINTAINER Miklos Argyelan [email protected]⁠

COPY simnibs_installer_linux.tar.gz .
RUN tar -xzf simnibs_installer_linux.tar.gz
RUN simnibs_installer/install -s
RUN mkdir /home/matlab/output
RUN chmod 777 /home/matlab/output

RUN sudo apt-get update && sudo apt-get install -y libglu1-mesa #gmsh gives error without this

ENTRYPOINT ["/home/matlab/SimNIBS-3.2/bin/headreco","all"]
CMD []
WORKDIR '/home/matlab/output'