Implementing CBIG_fMRI_Preproc2016 in a docker

This dockerfile includes CBIG_fMRI_Preproc2016, ANTS 2.2.0, AFNI, fsl-5.0.10, freesurfer-6.0.0, matlabruntime 2021a, and Connectome Workbench. A full license for freesurfer is needed and must be put in the dockerfile.

The image takes around 50 min to build if it is on a brand new machine In the dockerfile there is a command at the end to copy the freesurfer license into the image. The freesurfer license file is in the folder with the dockerfile. That will need to be changed depending on the machine

An example command to start the container in a bash is

docker run --name CBIG_docker --rm -i -t  -v /fileserver/gammu/collections/GSP:/BIDS_input -v /fileserver/gammu/projects/GSP/freesurfer_v4.5.0:/freesurfer_input -v /fileserver/gammu/projects/GSP_CBIG_docker:/output -v /fileserver/caladan_ssd/repos/CBIG_compiled/stable_projects/preprocessing/CBIG_fMRI_Preproc2016/utilities:/extra_files [docker image id/name] bash

The image id/name would need be changed based on the image created Once the container is started, run the setup_docker_CBIG.sh which is in the /CBIG_compiled-for-MCR folder The setup script, as of writing, changes the links for compiled m files and copies large compiled m files from caladan over to the docker image It also installs the directory for Connectome Workbench

An example command to run CBIG in bash is

/BIDS_to_CBIG_fMRI_Preproc2016/BIDS_2BP_docker_CBIG_fMRI_preprocess.sh \
/BIDS_input \
sub-0002 \
/freesurfer_input \
/output \
/BIDS_to_CBIG_fMRI_Preproc2016/configs/testing.config 

The folders for the inputs and outputs are based on the docker run command up above To see the logs with this command you can go to /output/CBIG_fMRI_preprocess_testing/sub-002/logs or on the server with /fileserver/gammu/projects/GSP_CBIG_docker/CBIG_fMRI_preprocess_testing/sub-0002/logs To redo a subject, if you want to delete the entire CBIG_fMRI_preprocess_testing folder you must delete it through the bash, it won’t let you through the server.

• One thing to note which is mentioned in the Mfile_log.md is that -censor needs to be added to the config file that you are using in CBIG_preproc_regress
• An error will occur saying CBIG_preproc_regress failed

• Remove spm and the matlab for it if it is decided that ultimately it is not needed
• Uncomment git-lfs if it is added to the main CBIG repo
• Change the CBIG_docker_setup.sh file in the CBIG compiled branch to remove the copy command for the files tracked by git-lfs
• In the Dockerfile remove the command to make the extra files folder since the files are not needed to copy over from the server