File transfer and management at mesocentre

identification to transfer files (also works with pharo/niolon to store on envau)
- add ssh key for mesocentre (cf. https://mesocentre.univ-amu.fr/copernicus) to ~/.ssh/ in home directory in pharo/niolon
- if needed, start ssh agent with eval "$(ssh-agent)" and add key with ssh-add ~/.ssh/<key_file>
- further information: link to mesocentre website
use scp or rsync to transfer files, for example
- copy fmriprep output files from mesocentre: scp -rp -P 8822 <username>@login.mesocentre.univ-amu.fr:/scratch/mgilson/braint/derivatives/fmriprep/<filename> <loca_dir>
- copy files to mesocentre: scp -rp -P 8822 <local_path_to_filename> <username>@login.mesocentre.univ-amu.fr:/scratch/mgilson/braint/<remote_path>
make aliases to mount/unmount remote directory (copy lines to .bashrc) using sshfs on ubuntu
- mount: alias mmeso='sshfs -p 8822 <username>@login.mesocentre.univ-amu.fr:/scratch/mgilson/braint/ -o auto_cache,reconnect <local_mount_dir>'
- unmount: alias umeso='fusermount -u <local_mount_dir>'
- if needed, install sshfs with apt or apt-get (sudo mode)
change file permissions of generated files to allow access for all group members:
- chmod -Rf 771 /scratch/mgilson/braint with '771' being read/write/execute for owner and group members, only execute for others
- chgrp -Rf <gp_id> /scratch/mgilson/braint where <gp_id> is the group number, 347 for BraINT

Preparation for fmriprep

create singularity image for fmriprep: singularity build /scratch/mgilson/braint/code/singularity/fmriprep-23.2.0.simg docker://nipreps/fmriprep:23.2.0
- check the latest version on https://fmriprep.org/en/stable/ to replace '23.2.0'
fixing jason description files for fmap: python3 fix_json_fmap.py in folder '/scratch/mgilson/braint/code/preproc/'
- link to script fix_json_fmap.py
- to use python on mesocentre, use module load python3 then python3 <script.py>

go to '/scratch/mgilson/braint/code/job_launch/' and simply execute sbatch sub-<idx>_fmriprep.sh with the index <idx> of the subject
- new launch scripts 'sub-_fmriprep.sh' for new subjects can be generated using gen_launch_scripts.py
- check progress using squeue -u <username> (your login for mesocentre)
- further information: link to mesocentre website

with conda: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
without conda: https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments
create requirement.txt file:
activate environment in slurm script: source <path-to-env>/activate