Merge pull request #35 from scitran-apps/parker-dev2

Parker dev2 [GEAR-142]

.dockerignore

@@ -0,0 +1,7 @@
+.git
+.DS_Store
+output/
+output2/
+config.json
+work/
+input/

.gitignore

@@ -0,0 +1,5 @@
+output/
+output2/
+config.json
+work/
+input/

Dockerfile

@@ -30,8 +30,16 @@ RUN apt-get update -qq \
     python \
     python-nibabel
 
+# Need to update pydicom
+RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
+    python get-pip.py
+
+COPY requirements.txt ./requirements.txt
+RUN pip install -r requirements.txt && rm -rf /root/.cache/pip
+
 # Compile DCM2NIIX from source
 ENV DCMCOMMIT=54cfd5176cb9f50c1c66d2f2e96beadf60e2edb4
+#ENV DCMCOMMIT=f54be46667fce7994d2062e2623d12253c1bd968
 RUN curl -#L  https://github.com/rordenlab/dcm2niix/archive/$DCMCOMMIT.zip | bsdtar -xf- -C /usr/local
 WORKDIR /usr/local/dcm2niix-${DCMCOMMIT}/build
 RUN cmake -DUSE_OPENJPEG=ON -MY_DEBUG_GE=ON ../ && \
@@ -42,9 +50,14 @@ RUN cmake -DUSE_OPENJPEG=ON -MY_DEBUG_GE=ON ../ && \
 ENV FLYWHEEL /flywheel/v0
 WORKDIR ${FLYWHEEL}
 
+## Copy in fix_dcm_vols
+ENV FIXDCMCOMMIT=918ee3327174c3c736e7b3839a556e0a709730c8
+RUN curl -#L https://raw.githubusercontent.com/VisionandCognition/NHP-Process-MRI/$FIXDCMCOMMIT/bin/fix_dcm_vols > ${FLYWHEEL}/fix_dcm_vols.py
+RUN chmod +x ${FLYWHEEL}/fix_dcm_vols.py
+
 # Add executables
 COPY run run_dcm2niix metadata.py coil_combine.py ./
-RUN chmod +x run metadata.py coil_combine.py
+RUN chmod 777 run metadata.py coil_combine.py fix_dcm_vols.py
 
 # Create Flywheel User
 RUN adduser --disabled-password --gecos "Flywheel User" flywheel

manifest.json

@@ -8,17 +8,17 @@
   "source": "https://github.com/scitran-apps/dcm2niix",
   "license": "BSD-2-Clause",
   "flywheel": "0",
-  "version": "0.7.9_1.0.20190410",
+  "version": "0.7.10_1.0.20190410",
   "custom": {
-    "docker-image": "scitran/dcm2niix:0.7.9_1.0.20190410",
+    "docker-image": "scitran/dcm2niix:0.7.10_1.0.20190410",
     "flywheel": {
       "uid": 1000,
       "gid": 1000,
       "suite": "SciTran"
     },
     "gear-builder": {
       "category": "converter",
-      "image": "scitran/dcm2niix:0.7.8_1.0.20190410"
+      "image": "scitran/dcm2niix:0.7.10_1.0.20190410"
     }
   },
   "config": {
@@ -113,6 +113,11 @@
       "description": "For sequences with individual coil data, saved as individual volumes, this option will save a NIfTI file with ONLY the combined coil data (i.e., the last volume). Default=False. Warning: We make no effort to check for independent coil data, we simply trust that if you have selcted this option you know what you are asking for.",
       "type": "boolean",
       "default": false
+    },
+    "remove_incomplete_volumes": {
+      "description": "Some 4D scans can be aborted mid-acquisition after any number of complete volume acquisitions.  The final volume may be incomplete, which causes problems during dcm2niix reconstruction.  Check this to scan the dicom archive before reconstruction and remove the files associated with the trailing incomplete volume.  All other volumes will be reconstructed as normal. ",
+      "type": "boolean",
+      "default": false
     }
   },
   "inputs": {

requirements.txt

@@ -0,0 +1 @@
+pydicom==1.3.0

run_dcm2niix

@@ -61,6 +61,7 @@ convert_only_series="$(parse_config 'convert_only_series')"
 lossless_scaling="$(parse_config 'lossless_scaling')"
 ignore_errors="$(parse_config 'ignore_errors')"
 coil_combine="$(parse_config 'coil_combine')"
+remove_incomplete_volumes="$(parse_config 'remove_incomplete_volumes')"
 
 
 ##############################################################################
@@ -162,6 +163,48 @@ else
   dicom_input=$INPUT_DIR
 fi
 
+
+##############################################################################################
+# Check to see if we need to remove dicoms from an incomplete volume for proper reconstruction
+if [[ ${remove_incomplete_volumes} == "true" ]]; then
+  echo $dicom_input
+
+  # Run the python script
+  echo "$CONTAINER Running incomplete volume correction"
+
+  echo dicoms before:
+  ls ${dicom_input}/*.dcm -1 | wc -l
+
+
+  python $FLYWHEEL_BASE/fix_dcm_vols.py ${dicom_input}
+  echo "$CONTAINER Complete"
+  # If it found missing volumes and worked succesfully, there will be a new directory in the original dicom input dir
+  # called "corrected_dcm"
+  echo "$CONTAINER Checking for files"
+  corrected_output=${dicom_input}/orphan_dcm
+  if [[ -d $corrected_output ]]; then
+    echo "$CONTAINER removed incomplete volumes from scan"
+    # For the sake of flywheel's naming, remove the orphan dcms
+    rm -rf ${dicom_input}/orphan_dcm
+
+    # and remove any DCM's still in the original directory (should be zero if python code works correctly)
+    rm  ${dicom_input}/*.dcm
+
+    # move back all the corrected images to the original directory
+    mv ${dicom_input}/corrected_dcm/*.dcm ${dicom_input}
+
+    # Remove the corrected directory
+    rm -rf ${dicom_input}/corrected_dcm
+
+    # Give report of dicoms after.
+    echo dicoms after:
+    ls ${dicom_input}/*.dcm -1 | wc -l
+
+  else
+    echo "$CONTAINER Attempted to run incomplete volume correction, but no correction was made"
+  fi
+fi
+
 echo -e "$CONTAINER $dicom_input"
 
 ##############################################################################