diff --git a/models/fmcib_radiomics/config/default.yml b/models/fmcib_radiomics/config/default.yml index cc4b1559..297a8a14 100644 --- a/models/fmcib_radiomics/config/default.yml +++ b/models/fmcib_radiomics/config/default.yml @@ -1,21 +1,22 @@ general: data_base_dir: /app/data version: 1.0 - description: "FMCIB pipeline" + description: FMCIB pipeline starting from DICOM files and centroids in json files or slicer exports named by their SeriesInstanceUID execute: -- FileStructureImporter -- CentroidExtractor +- DicomImporter +- FileImporter +- NiftiConverter - FMCIBRunner - DataOrganizer modules: - FileStructureImporter: - structures: - - $patientID/CT.nrrd@instance@nrrd:mod=ct - - $patientID/masks/GTV-1.nrrd@nrrd:mod=seg - import_id: patientID + + FileImporter: + instance_id: sid + meta: type=fmcibcoordinates + type: json DataOrganizer: targets: - - json:type=fmcibfeatures-->[i:patientID]/features.json \ No newline at end of file + - json:type=fmcibfeatures-->[i:sid]/features.json \ No newline at end of file diff --git a/models/fmcib_radiomics/config/dicom.yml b/models/fmcib_radiomics/config/dicom.yml deleted file mode 100644 index da7dc513..00000000 --- a/models/fmcib_radiomics/config/dicom.yml +++ /dev/null @@ -1,22 +0,0 @@ -general: - data_base_dir: /app/data - version: 1.0 - description: FMCIB pipeline starting from DICOM files and centroids in json files named by their SeriesInstanceUID - -execute: -- DicomImporter -- FileImporter -- NiftiConverter -- FMCIBRunner -- DataOrganizer - -modules: - - FileImporter: - instance_id: sid - meta: type=fmcibcoordinates - type: json - - DataOrganizer: - targets: - - json:type=fmcibfeatures-->[i:sid]/features.json \ No newline at end of file diff --git a/models/fmcib_radiomics/config/from_nrrd_mask.yml b/models/fmcib_radiomics/config/from_nrrd_mask.yml new file mode 100644 index 00000000..22644ffc --- /dev/null +++ b/models/fmcib_radiomics/config/from_nrrd_mask.yml @@ -0,0 +1,21 @@ +general: + data_base_dir: /app/data + version: 1.0 + description: "FMCIB pipeline starting from a nrrd file image and a nnrd binary mask of the GTV." + +execute: +- FileStructureImporter +- CentroidExtractor +- FMCIBRunner +- DataOrganizer + +modules: + FileStructureImporter: + structures: + - $patientID/CT.nrrd@instance@nrrd:mod=ct + - $patientID/masks/GTV-1.nrrd@nrrd:mod=seg + import_id: patientID + + DataOrganizer: + targets: + - json:type=fmcibfeatures-->[i:patientID]/features.json \ No newline at end of file