diff --git a/models/gc_lunglobes/config/default.yml b/models/gc_lunglobes/config/default.yml index f25f0444..6df165fb 100644 --- a/models/gc_lunglobes/config/default.yml +++ b/models/gc_lunglobes/config/default.yml @@ -7,7 +7,6 @@ execute: - DicomImporter - MhaConverter - LobeSegmentationRunner -- NiftiConverter - DsegConverter - DataOrganizer @@ -20,10 +19,7 @@ modules: mod: ct MhaConverter: - engine: plastimatch - - NiftiConverter: - in_datas: mha:mod=seg + engine: panimg DsegConverter: model_name: GCLungLobes diff --git a/models/gc_lunglobes/dockerfiles/Dockerfile b/models/gc_lunglobes/dockerfiles/Dockerfile index 66f5a9ca..0e87d31a 100644 --- a/models/gc_lunglobes/dockerfiles/Dockerfile +++ b/models/gc_lunglobes/dockerfiles/Dockerfile @@ -1,7 +1,7 @@ FROM mhubai/base:latest # Update authors label -LABEL authors="s.vandeleemput@radboudumc.nl,dbontempi@bwh.harvard.edu,lnuernberg@bwh.harvard.edu" +LABEL authors="sil.vandeleemput@radboudumc.nl,dbontempi@bwh.harvard.edu,lnuernberg@bwh.harvard.edu" # Install system dependencies for OpenCV RUN apt-get update && apt-get install ffmpeg libsm6 libxext6 -y @@ -19,8 +19,8 @@ RUN pip3 install --no-cache-dir --force-reinstall SimpleITK==1.2.4 ARG MHUB_MODELS_REPO RUN buildutils/import_mhub_model.sh gc_lunglobes ${MHUB_MODELS_REPO} -# Install Xie's pulmonary lobe segmentation algorithm and model weights -RUN git clone https://github.com/DIAGNijmegen/bodyct-pulmonary-lobe-segmentation.git src && \ +# Install Xie's pulmonary lobe segmentation algorithm and model weights (release gclobe165 v1.6.5) +RUN git clone --depth 1 --branch v1.6.5 https://github.com/DIAGNijmegen/bodyct-pulmonary-lobe-segmentation.git src && \ sed -i 's/from models import CTSUNet/from src.models import CTSUNet/g' src/test.py # Default run script diff --git a/models/gc_lunglobes/meta.json b/models/gc_lunglobes/meta.json index 47229053..d5d530a1 100644 --- a/models/gc_lunglobes/meta.json +++ b/models/gc_lunglobes/meta.json @@ -10,7 +10,7 @@ "format": "DICOM", "modality": "CT", "bodypartexamined": "Chest", - "slicethickness": "2.5mm", + "slicethickness": "0.75mm", "non-contrast": true, "contrast": false } ], @@ -26,7 +26,7 @@ } ], "model": { "architecture": "Relational two-stage U-net", - "training": "Supervised", + "training": "supervised", "cmpapproach": "3D" }, "data": { @@ -36,7 +36,7 @@ "evaluation": { "vol_samples": 1155 }, - "public": "Partially", + "public": false, "external": true } }, @@ -46,9 +46,9 @@ "devteam": "DIAGNijmegen (Diagnostic Image Analysis Group, Radboud UMC, The Netherlands)", "type": "Relational two-stage U-Net (Cascade of two relational U-Net, trained end-to-end)", "date": { - "weights": "14/02/22", - "code": "n/a", - "pub": "n/a" + "weights": "2022-02-14", + "code": "2023-11-27", + "pub": "2020-05-15" }, "cite": "W. Xie, C. Jacobs, J. -P. Charbonnier and B. van Ginneken, 'Relational Modeling for Robust and Efficient Pulmonary Lobe Segmentation in CT Scans,' in IEEE Transactions on Medical Imaging, vol. 39, no. 8, pp. 2664-2675, Aug. 2020, doi: 10.1109/TMI.2020.2995108.", "license": {