From a034e85ba5f40a33f4e0fe71ac96a242c09d8a97 Mon Sep 17 00:00:00 2001
From: marcobarilari <38101692+marcobarilari@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:09:51 +0200
Subject: [PATCH] Update cpp_fmriprep.slurm

---
 doc/cpp_fmriprep.slurm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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 \