From 0fe8183a70c2062656578c9f039809dd1c8bf18c Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Wed, 2 Aug 2023 18:02:02 +0200 Subject: [PATCH 1/6] update e-mailaddress and cleanup/simplify default.yml --- models/gc_lunglobes/config/default.yml | 6 +----- models/gc_lunglobes/dockerfiles/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/models/gc_lunglobes/config/default.yml b/models/gc_lunglobes/config/default.yml index b30cbf9c..1bfe2981 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 @@ -19,11 +18,8 @@ modules: meta: mod: ct - NiftiConverter: - targets: - - mha:mod=seg - DsegConverter: + source_segs: [mha:mod=seg:roi=*] dicomseg_json_path: /app/models/xie2020_lobe_segmentation/config/dseg.json skip_empty_slices: True diff --git a/models/gc_lunglobes/dockerfiles/Dockerfile b/models/gc_lunglobes/dockerfiles/Dockerfile index fe182e44..92e1b4e5 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 From f081bd3065e536c4adc6ee0b9278845df5a7ea23 Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Wed, 2 Aug 2023 23:07:45 +0200 Subject: [PATCH 2/6] removed redundant line source_segs from DsegConverter in default.yml --- models/gc_lunglobes/config/default.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/models/gc_lunglobes/config/default.yml b/models/gc_lunglobes/config/default.yml index 1bfe2981..e3e0b03a 100644 --- a/models/gc_lunglobes/config/default.yml +++ b/models/gc_lunglobes/config/default.yml @@ -19,7 +19,6 @@ modules: mod: ct DsegConverter: - source_segs: [mha:mod=seg:roi=*] dicomseg_json_path: /app/models/xie2020_lobe_segmentation/config/dseg.json skip_empty_slices: True From 0ad89310a31f51a6c82002d67e947ba7377b7227 Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Wed, 13 Sep 2023 10:41:58 +0200 Subject: [PATCH 3/6] add specific commit hash for algorithm main branch at 2023/09/13 --- models/gc_lunglobes/dockerfiles/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/models/gc_lunglobes/dockerfiles/Dockerfile b/models/gc_lunglobes/dockerfiles/Dockerfile index 92e1b4e5..fab5ca99 100644 --- a/models/gc_lunglobes/dockerfiles/Dockerfile +++ b/models/gc_lunglobes/dockerfiles/Dockerfile @@ -23,8 +23,9 @@ RUN git stash \ && git sparse-checkout set "models/gc_lunglobes" \ && git fetch https://github.com/MHubAI/models.git main -# Install Xie's pulmonary lobe segmentation algorithm and model weights +# Install Xie's pulmonary lobe segmentation algorithm and model weights (main branch commit at 2023/09/13) RUN git clone https://github.com/DIAGNijmegen/bodyct-pulmonary-lobe-segmentation.git src && \ + cd src && git reset --hard 5a64b70504d46c042c30851a69cec370f1202e67 && cd /app && \ sed -i 's/from models import CTSUNet/from src.models import CTSUNet/g' src/test.py # Default run script From 0e449b814a7cc14d03d44fa0504438d2411dd11e Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Tue, 28 Nov 2023 11:24:37 +0100 Subject: [PATCH 4/6] update algorithm version to release gclobe165 with fix for #69 --- models/gc_lunglobes/dockerfiles/Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/models/gc_lunglobes/dockerfiles/Dockerfile b/models/gc_lunglobes/dockerfiles/Dockerfile index 1343e6bb..0e87d31a 100644 --- a/models/gc_lunglobes/dockerfiles/Dockerfile +++ b/models/gc_lunglobes/dockerfiles/Dockerfile @@ -19,9 +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 (main branch commit at 2023/09/13) -RUN git clone https://github.com/DIAGNijmegen/bodyct-pulmonary-lobe-segmentation.git src && \ - cd src && git reset --hard 5a64b70504d46c042c30851a69cec370f1202e67 && cd /app && \ +# 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 From c25f532b1880f6c2f52848ee61db7cb33412a625 Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Tue, 27 Feb 2024 16:10:43 +0100 Subject: [PATCH 5/6] meta.json - update date formats, data.public, and model.training fields --- models/gc_lunglobes/meta.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/models/gc_lunglobes/meta.json b/models/gc_lunglobes/meta.json index 47229053..a1fdc8c2 100644 --- a/models/gc_lunglobes/meta.json +++ b/models/gc_lunglobes/meta.json @@ -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": { From 37a7cae4da9d21b2857dec4ccaf292fb6b33cc85 Mon Sep 17 00:00:00 2001 From: silvandeleemput Date: Mon, 4 Mar 2024 14:46:01 +0100 Subject: [PATCH 6/6] meta.json - made public field a boolean, changed slice thickness to 0.75mm --- models/gc_lunglobes/meta.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/models/gc_lunglobes/meta.json b/models/gc_lunglobes/meta.json index a1fdc8c2..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 } ], @@ -36,7 +36,7 @@ "evaluation": { "vol_samples": 1155 }, - "public": "false", + "public": false, "external": true } },