Ignore OSX-generated subfolders found in the archive

manifest.json

@@ -8,9 +8,9 @@
   "source": "https://github.com/scitran-apps/dcm2niix",
   "license": "BSD-2-Clause",
   "flywheel": "0",
-  "version": "0.7.5_1.0.20180622_5af76a9",
+  "version": "0.7.6_1.0.20180622_5af76a9",
   "custom": {
-    "docker-image": "scitran/dcm2niix:0.7.5_1.0.20180622_5af76a9",
+    "docker-image": "scitran/dcm2niix:0.7.6_1.0.20180622_5af76a9",
     "flywheel": {
       "uid": 1000,
       "gid": 1000

run_dcm2niix

@@ -95,15 +95,15 @@ if [[ "$input_file" == *.zip ]] ; then
   echo "$CONTAINER  Unzipping $input_file"
   unzip -q -B "$input_file" -d $INPUT_DIR
 
-  # Find unzipped directory in input dir
-  dicom_input=$(find $INPUT_DIR/* -not -path '*/\.*' -type d | head -1)
+  # Find unzipped sub-directory within the input directory
+  dicom_input=$(find $INPUT_DIR/* -not -path '*/\.*' -not -path '__MACOSX' -type d | head -1)
 
-  # If there is no unzipped directory, check for PAR/REC files
+  # If there is no unzipped sub-directory, check for PAR/REC files at the top-level
   if [[ -z "$dicom_input" ]]; then
       dicom_input=$(find $INPUT_DIR/* -not -path '*/\.*' -type f -name "*.par" -o -name "*.PAR" | head -1)
   fi
 
-  # Zip bomb: Set dicom_input to INPUT_DIR
+  # Zip bomb: DICOMS are at the top level -- set dicom_input to INPUT_DIR
   if [[ -z "$dicom_input" ]]; then
     dicom_input=$INPUT_DIR
   fi