Merge pull request #26 from cpp-lln-lab/marco_update-fmriprep-slurm-p…

…aram

Update cpp_fmriprep.slurm

doc/cpp_fmriprep.slurm

@@ -4,8 +4,8 @@
 #SBATCH --time=9:00:00 # hh:mm:ss
 
 #SBATCH --ntasks=1
-#SBATCH --cpus-per-task=9
-#SBATCH --mem-per-cpu=10000 # megabytes
+#SBATCH --cpus-per-task=4
+#SBATCH --mem-per-cpu=20000 # megabytes
 #SBATCH --partition=batch,debug
 
 #SBATCH --mail-user=marco.barilari@uclouvain.be
@@ -14,10 +14,10 @@
 
 #SBATCH --comment=project-name
 
-#export OMP_NUM_THREADS=9
-#export MKL_NUM_THREADS=9
+#export OMP_NUM_THREADS=4
+#export MKL_NUM_THREADS=4
 
-## CPP frmiprep script for CECI cluster
+## CPP frmiprep script for CECI cluster v0.2.0
 #
 # writtent by CPP people
 #
@@ -62,7 +62,7 @@ subjID=$1
 TaskName=$2
 
 # "latest" or procide specific version number
-FMRIPREP_VERSION="23.1.4"
+FMRIPREP_VERSION="24.0.0"
 
 # set username to locate scratch folder
 ceci_username="marcobar"
@@ -87,15 +87,15 @@ singularity run --cleanenv \
     -B "${bids_dir}":/bids_dir \
     -B "${output_dir}":/output \
     -B "${freesurfer_license_folder}":/freesurfer_license \
-        "${path_to_singularity_image}" \
-            /bids_dir \
-            /output \
-            participant --participant-label "${subjID}" \
-            --task "${TaskName}" \
-            --work-dir /scratch_dir/work-fmriprep \
-            --fs-license-file /freesurfer_license/license.txt \
-            --output-spaces MNI152NLin2009cAsym T1w \
-            --dummy-scans ${nb_dummy_scans} \
-            --notrack \
-            --skip_bids_validation \
-            --stop-on-first-crash
+    "${path_to_singularity_image}" \
+    /bids_dir \
+    /output \
+    participant --participant-label "${subjID}" \
+    --task "${TaskName}" \
+    --work-dir /scratch_dir/work-fmriprep/"${subjID}" \
+    --fs-license-file /freesurfer_license/license.txt \
+    --output-spaces MNI152NLin2009cAsym T1w \
+    --dummy-scans ${nb_dummy_scans} \
+    --notrack \
+    --skip_bids_validation \
+    --stop-on-first-crash