From 87cfcdf9e4f26cb614b8bba199317d541decd2f4 Mon Sep 17 00:00:00 2001
From: Michael Perry <lmperry@stanford.edu>
Date: Fri, 10 Feb 2017 15:04:40 -0800
Subject: [PATCH 1/3] parse config options with raw jq output

closes #2
---
 run | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/run b/run
index d7cbe35..84a67c9 100755
--- a/run
+++ b/run
@@ -46,15 +46,15 @@ LOG_FILE=/flywheel/v0/output/mri-deface.log
           if [[ -e $CONFIG_FILE ]]
               then
                   echo "Config file is present"
-                  outextension=`cat $CONFIG_FILE | jq '.config.output_extension'`
+                  outextension=`cat $CONFIG_FILE | jq -r '.config.output_extension'`
                   echo "The extension read from the config file: $outextension"
               # Otherwise, define output file extension as nifti (.nii.gz)
               else
-                  outextension="nii.gz"
+                  outextension=".nii.gz"
                   echo "No config file found, so default extension ($outextension) is being used for output"
           fi
           # Define output file to be passed to mri_deface
-          output_file=$OUTPUT_DIR/$filename'_deface.'$outextension
+          output_file=$OUTPUT_DIR/$filename'_deface'$outextension
           /flywheel/v0/mri_deface $input_file $brain_template $face_template $output_file
       else
           echo "No Nifti, DICOM or MGZ inputs were found within input directory $INPUT_DIR"

From 8d91ae19406da7f53e58450e23d98a9bd8e20457 Mon Sep 17 00:00:00 2001
From: Michael Perry <lmperry@stanford.edu>
Date: Fri, 10 Feb 2017 15:07:57 -0800
Subject: [PATCH 2/3] increment version number

---
 export.sh     | 2 +-
 manifest.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/export.sh b/export.sh
index fd9d35f..9768259 100755
--- a/export.sh
+++ b/export.sh
@@ -2,7 +2,7 @@
 # Exports the container in the cwd.
 # The container can be exported once it's started with
 
-version=0.1.1
+version=0.1.2
 outname=mri_deface-$version.tar
 container=mri_deface
 image=flywheel/mri-deface
diff --git a/manifest.json b/manifest.json
index 6ce3980..9f596d4 100644
--- a/manifest.json
+++ b/manifest.json
@@ -26,7 +26,7 @@
     "name": "mri-deface",
     "source": "https://github.com/flywheel-apps/mri-deface",
     "url": "https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "custom": {
       "docker-image": "flywheel/mri-deface:v0.1.1"
     }

From fecec3cf67ef82978ae84be2796a978cd917906e Mon Sep 17 00:00:00 2001
From: Michael Perry <lmperry@stanford.edu>
Date: Mon, 13 Feb 2017 07:52:05 -0800
Subject: [PATCH 3/3] update docker-image version

---
 manifest.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/manifest.json b/manifest.json
index 9f596d4..1f67945 100644
--- a/manifest.json
+++ b/manifest.json
@@ -28,6 +28,6 @@
     "url": "https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface",
     "version": "0.1.2",
     "custom": {
-      "docker-image": "flywheel/mri-deface:v0.1.1"
+      "docker-image": "flywheel/mri-deface:v0.1.2"
     }
 }