ENH: DICOM To NRRD Module Implementation

CMakeLists.txt

@@ -23,6 +23,7 @@ add_subdirectory(AutoSave)
 add_subdirectory(CharacterizeTransformMatrix)
 add_subdirectory(CombineModels)
 add_subdirectory(CurvedPlanarReformat)
+add_subdirectory(DICOMToNRRD)
 add_subdirectory(DocumentationTools)
 if (Slicer_VERSION VERSION_LESS 5.1)
   # Latest Slicer 5.1 and above has ITK-Snap Label Description File importer built in

DICOMToNRRD/CMakeLists.txt

@@ -0,0 +1,27 @@
+#-----------------------------------------------------------------------------
+set(MODULE_NAME DICOMToNRRD)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  # Royalty free CPU icon retrieved from https://publicdomainvectors.org/
+  Resources/Icons/${MODULE_NAME}.png
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  WITH_GENERIC_TESTS
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+  # run ctest -C Release -R py_DICOMToNRRD -VV in Slicer-build to test this out individually
+  slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
+
+endif()

DICOMToNRRD/DICOM To NRRD Slicer Test Cases.csv

@@ -0,0 +1,12 @@
+Test Case #,Description,“Create DICOM information file/s” Checked? Y / N," ""NRRD Scalar Volumes Only"" Checked ? Y / N",# NRRD Files Generated,# PatientDICOMInfo.json Files Generated,Data Description URI,Date Tested
+1,I tested 5 / 126 Liver Cancer B-mode-and-CEUS-Liver scans,Y,N,5,5,https://www.cancerimagingarchive.net/collection/b-mode-and-ceus-liver/,06/26/24
+2,I tested 5 / 126 Liver Cancer B-mode-and-CEUS-Liver scans,N,Y,5,0,https://www.cancerimagingarchive.net/collection/b-mode-and-ceus-liver/,06/26/24
+3,I tested ReMIND-001,Y,Y,6,6,https://www.cancerimagingarchive.net/collection/remind/,06/26/24
+4,I tested ReMIND-001,N,N,6,0,https://www.cancerimagingarchive.net/collection/remind/,06/26/24
+5,I tested folder 144126-210-T-1637,Y,Y,2,2,https://www.cancerimagingarchive.net/collection/pdmr-texture-analysis/,06/26/24
+6,I tested folder CMB-MML-MSB-07473,N,N,1,1,https://www.cancerimagingarchive.net/collection/cmb-mml/,06/26/24
+7,I tested 105 random DICOM scans,Y,Y,105,105,https://www.cancerimagingarchive.net/browse-collections/,06/26/24
+8,I tested C3N-02715,N,N,7,7,https://www.cancerimagingarchive.net/collection/cptac-luad/,06/26/24
+9,I tested 500 scans from NLST,Y,Y,500,500,https://www.cancerimagingarchive.net/collection/nlst/,06/26/24
+10,Tested one folder CMB-MML-MSB-01103,Y,Y,8,8,https://www.cancerimagingarchive.net/collection/cmb-mml/,12/06/24
+11,Tested the whole CMB-MML folder,Y,N,186,186,https://www.cancerimagingarchive.net/collection/cmb-mml/,12/06/24

README.md

@@ -207,3 +207,22 @@ Example module that allows opening a file in 3D Slicer by clicking on a link in
 Example links that open image and/or segmentation in 3D Slicer:
 - LungCTAnalyzerChestCT image: `slicer://viewer/?download=https%3A%2F%2Fgithub.com%2Frbumm%2FSlicerLungCTAnalyzer%2Freleases%2Fdownload%2FSampleData%2FLungCTAnalyzerChestCT.nrrd`
 - LungCTAnalyzerChestCT image + segmentation" `slicer://viewer/?show3d=true&segmentation=https%3A%2F%2Fgithub.com%2Frbumm%2FSlicerLungCTAnalyzer%2Freleases%2Fdownload%2FSampleData%2FLungCTAnalyzerMaskSegmentation.seg.nrrd&image=https%3A%2F%2Fgithub.com%2Frbumm%2FSlicerLungCTAnalyzer%2Freleases%2Fdownload%2FSampleData%2FLungCTAnalyzerChestCT.nrrd`
+
+## DICOMToNRRD
+
+The DICOM To NRRD module provides batch processing for converting DICOM files into NRRD files and outputs the files into a DICOM standard conforming folder hierarchy of Patient/Study/Series. Nearly Raw Raster Data (NRRD) was developed by Professor Gordon Kindlmann: https://people.cs.uchicago.edu/~glk/software/ 
+
+![image](DICOMToNRRD/Resources/DICOMToNRRD.png)
+
+### Tutorial
+
+- Click the magnifying glass next to "Modules:" (near the top left of the window)
+- Scroll down and click `DICOM To NRRD`
+- Ensure the Parameters window is expanded (you may need to click the arrow to the left of Parameters)
+- Select an input DICOM directory
+- Select an output NRRD directory
+- Optionally uncheck "NRRD Scalar Volumes Only:"
+- Optionally uncheck "Create DICOM metadata file/s:"
+- Click Process button to convert DICOM files to NRRD files
+- Wait for the popup window: "DICOM to NRRD processing finished" and then click OK
+- The outputted DICOM NRRD directory shall contain a hierarchy of Patient/Study/Series folders each with a NRRD file