Add files via upload

Author: andrewjahn

fmriprep_Scripted.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+subject=$1
+
+  #User inputs:
+  bids_root_dir=$HOME/Desktop/Flanker
+  subj=$subject
+  nthreads=4
+  mem=20 #gb
+  container=docker #docker or singularity
+
+  #Begin:
+
+  #Convert virtual memory from gb to mb
+  mem=`echo "${mem//[!0-9]/}"` #remove gb at end
+  mem_mb=`echo $(((mem*1000)-5000))` #reduce some memory for buffer space during pre-processing
+
+  #export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
+  export FS_LICENSE=$HOME/Desktop/Flanker/derivatives/license.txt
+
+  #Run fmriprep
+  if [ $container == singularity ]; then
+    unset PYTHONPATH; singularity run -B $HOME/.cache/templateflow:/opt/templateflow $HOME/fmriprep.simg \
+      $bids_root_dir $bids_root_dir/derivatives \
+      participant \
+      --participant-label $subj \
+      --skip-bids-validation \
+      --md-only-boilerplate \
+      --fs-license-file $HOME/Desktop/Flanker/derivatives/license.txt \
+      --fs-no-reconall \
+      --output-spaces MNI152NLin2009cAsym:res-2 \
+      --nthreads $nthreads \
+      --stop-on-first-crash \
+      --mem_mb $mem_mb \
+      -w $HOME
+  else
+    fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
+      participant \
+      --participant-label $subj \
+      --skip-bids-validation \
+      --md-only-boilerplate \
+      --fs-license-file $HOME/Desktop/Flanker/derivatives/license.txt \
+      --fs-no-reconall \
+      --output-spaces MNI152NLin2009cAsym:res-2 \
+      --nthreads $nthreads \
+      --stop-on-first-crash \
+      --mem_mb $mem_mb \
+      -w $HOME
+  fi