Merge pull request #19 from marcobarilari/marco_small-fixies

last fixes to run fmriprep

Author: marcobarilari

doc/cpp_fmriprep.slurm

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 #SBATCH --job-name=fMRIprep
-#SBATCH --time=09:00:00 # hh:mm:ss
+#SBATCH --time=00:05:00 # hh:mm:ss
 
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=6
@@ -10,7 +10,7 @@
 
 #SBATCH --mail-user=marco.barilari@uclouvain.be
 #SBATCH --mail-type=ALL
-#SBATCH --output=$HOME/jobs_report/fmriprep_job-%j.txt
+#SBATCH --output=/home/ucl/irsp/marcobar/jobs_report/fmriprep_job-%j.txt
 
 #SBATCH --comment=project-name
 

doc/run_fmriprep.md

@@ -49,7 +49,8 @@ Content of the `cpp_fmriprep.slurm` file (download and edit from [here](cpp_fmri
 !!! Warning
 
     1. Read the fmriprep documentation to know what you are doing and how the arguments of the run call effects the results
-    2. Edit the scripts with the info you need to make it run for your user (check the paths and the `username` etc.)
+    2. All the paths and email are set afte Marco's users for demosntration. 
+    3. Edit the scripts with the info you need to make it run for your user from top to buttom of the script, do not over look the first "commented" chunk cause it is not a real commented section (check the email and job report path, data paths and the `username` etc.). 
 
 ```bash
 {% include "cpp_fmriprep.slurm" %}