Merge pull request #3 from flywheel-apps/v0.1.2

V0.1.2

Author: lmperry

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

manifest.json

@@ -26,8 +26,8 @@
     "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"
+      "docker-image": "flywheel/mri-deface:v0.1.2"
     }
 }

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"