diff --git a/doc/cpp_fmriprep.slurm b/doc/cpp_fmriprep.slurm index 44d0e90..5f4f9aa 100644 --- a/doc/cpp_fmriprep.slurm +++ b/doc/cpp_fmriprep.slurm @@ -38,9 +38,9 @@ # - multipple tasks # sbatch cpp_fmriprep.sh sub-01 'visMotLocalizer audMotLocalizer' -# create output and jobs_report folders in case they don't exist -mkdir -p "${output_dir}" +# create jobs_report and output folders in case they don't exist mkdir -p $HOME/jobs_report/ +mkdir -p "${output_dir}" # fail whenever something is fishy # -e exit immediately @@ -69,6 +69,7 @@ bids_dir="$HOME/fmriprep_trial/raw" output_dir="$HOME/fmriprep_trial/derivatives/fmriprep" freesurfer_license_folder="$HOME/tools/freesurfer_license" +# make the scratch folder, here there is no limit space and fmriprep can store stuff in case of crash and do not start from zero again mkdir -p "${scratch_dir}"/work-fmriprep singularity run --cleanenv \