henryburgess/hcppipelines repository overview

⁠HCP Pipelines

⁠Usage

1. Export any storage required for accessing data during the job (Note: This example makes the HOME, and STORAGE1 paths available during the job): export STORAGE1=/storage1/fs1/<RIS directory>, export LSF_DOCKER_VOLUMES="$HOME:$HOME $STORAGE1:$STORAGE1"

2. Start the job: bsub -R 'gpuhost' -R "rusage[mem=32GB]" -n 16 -Is -q general-interactive -a 'docker(henryburgess/hcppipelines)' /bin/bash

3. Activate the included Python venv: source /opt/venv/bin/activate

4. Run any setup prior to running the bash script. Check that all PATH variables have been set correctly. If not, run the following command: PATH=/opt/venv/bin:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/connectome-workbench/workbench/bin_linux64:/usr/local/msm_hocr:/usr/local/mrtrix3/bin:/usr/local/ants/bin:/usr/local/c3d/bin:/usr/local/MATLAB_Runtime_R2022a_Update_9_glnxa64/v912/bin:$PATH

5. Execute the bash script: ./script.sh

⁠Troubleshooting

• Ensure the FS_LICENSE environment variable is set after starting the container. If not, run: FS_LICENSE=/usr/local/freesurfer/license.txt