From b8fc9cae4d68e6b203b1b846ac657698e7d7f979 Mon Sep 17 00:00:00 2001
From: Jake Palmer <jake.palmer@sydney.edu.au>
Date: Wed, 26 Aug 2020 10:51:37 +1000
Subject: [PATCH] Check if required inputs exist in pipeline.sh

---
 src/pipeline.sh | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 mode change 100644 => 100755 src/pipeline.sh

diff --git a/src/pipeline.sh b/src/pipeline.sh
old mode 100644
new mode 100755
index edb46f1..2540561
--- a/src/pipeline.sh
+++ b/src/pipeline.sh
@@ -19,6 +19,21 @@ export PATH=$PATH:$ANTSPATH:/extra/ANTS/ANTs/Scripts
 # Set up pytorch
 source /extra/pytorch/bin/activate
 
+# Check input
+if [[ ! -f /INPUTS/b0.nii.gz ]]; then
+	echo ERROR: Could not find required input /INPUTS/b0.nii.gz
+	exit 
+elif [[ ! -f /INPUTS/T1.nii.gz ]]; then
+	echo ERROR: Could not find required input /INPUTS/T1.nii.gz
+	exit
+elif [[ ! -f /INPUTS/acqparams.txt ]]; then
+	echo ERROR: Could not find required input /INPUTS/acqparams.txt
+	exit
+elif [[ ! -f /extra/freesurfer/license.txt ]]; then
+	echo ERROR: Could not find required /extra/freesurfer/license.txt
+	exit
+fi
+
 # Prepare input
 prepare_input.sh /INPUTS/b0.nii.gz /INPUTS/T1.nii.gz /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c.nii.gz /extra/atlases/mni_icbm152_t1_tal_nlin_asym_09c_2_5.nii.gz /OUTPUTS