Merge pull request #42 from DIAGNijmegen/m-gc-lobesegmentation-xie

MHub / GC - Minor cleanup gc_lunglobes
MHubAI · Mar 4, 2024 · dc3698c · dc3698c
2 parents 510b6a6 + 37a7cae
commit dc3698c
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Showing 3 changed files with 10 additions and 14 deletions.
diff --git 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
@@ -1,7 +1,7 @@
 FROM mhubai/base:latest
 
 # Update authors label
-LABEL authors="s[email protected],[email protected],[email protected]"
+LABEL authors="sil[email protected],[email protected],[email protected]"
 
 # 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
@@ -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": {