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MHub / GC - Add GC nnUNet Pancreas model #39

Merged
merged 25 commits into from
Feb 28, 2024
Merged

MHub / GC - Add GC nnUNet Pancreas model #39

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0d7ec9d
WIP initial pancreas_pdac model commit
silvandeleemput Jul 4, 2023
af79adb
renamed nnunet_pancreas_pdac -> gc_nnunet_pancreas, addded run script…
silvandeleemput Jul 20, 2023
4bb7483
update for new base image, add dseg.json for class labels
silvandeleemput Aug 1, 2023
3be3473
Merge branch 'main' into m-gc-nnunet-pancreas
silvandeleemput Aug 1, 2023
12f30d8
cleanup code runner and run, configure dsegconverter, dataorganizer
silvandeleemput Aug 1, 2023
16d1893
add panimg backend for mhaconverter and cleanup
silvandeleemput Aug 30, 2023
aef205a
Merge branch 'MHubAI:main' into m-gc-nnunet-pancreas
silvandeleemput Sep 14, 2023
19d29d8
Updated and cleaned Dockerfile and Runner and added some comments
silvandeleemput Sep 14, 2023
790133a
Merge branch 'MHubAI:main' into m-gc-nnunet-pancreas
silvandeleemput Oct 10, 2023
737a5d2
add meta.json
silvandeleemput Oct 10, 2023
b04fb7e
Merge branch 'MHubAI:main' into m-gc-nnunet-pancreas
silvandeleemput Nov 23, 2023
334d573
update mhub model definition import Dockerfile
silvandeleemput Nov 23, 2023
4466e56
removed first comment line in Dockerfile
silvandeleemput Nov 23, 2023
2b035fe
Added segdb export, removed dseg.json, added remapped output to runne…
silvandeleemput Dec 7, 2023
a56e860
add cli for running the pdac_detection model
silvandeleemput Dec 7, 2023
713b0f3
added VEIN,ARTERY rois to output segmentation, cleaned config and run…
silvandeleemput Dec 12, 2023
55e34cf
add comments to CLI, add clean method and case-level likelihood extra…
silvandeleemput Jan 15, 2024
9c9508d
meta.json - update analysis section and evaluation data section #39
silvandeleemput Jan 15, 2024
4969367
updated model/algorithm version to latest commit, removed manual code…
silvandeleemput Jan 16, 2024
1b24825
meta.json - match model name #39
silvandeleemput Jan 16, 2024
561883b
meta.json - added disclaimer for output segmentation map
silvandeleemput Jan 18, 2024
2df25f3
updated to lastest version of algorithm, changed to output the raw he…
silvandeleemput Feb 1, 2024
f189937
meta.json - moved segmentation disclaimer to description and modified…
silvandeleemput Feb 1, 2024
726fdcb
fix dependencies conflict new base image #39
silvandeleemput Feb 8, 2024
343c6ab
meta.json - added version 0.1.0 to details
silvandeleemput Feb 26, 2024
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21 changes: 11 additions & 10 deletions models/gc_nnunet_pancreas/meta.json
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Expand Up @@ -17,16 +17,6 @@
}
],
"outputs": [
{
"type": "Segmentation",
"classes": [
"veins",
"arteries",
"pancreas",
"pancreatic duct",
"bile duct"
]
},
{
"type": "Prediction",
"valueType": "Likelihood map",
Expand All @@ -40,6 +30,17 @@
"label": "Pancreatic tumor likelihood",
"description": "Case-level pancreatic tumor likelihood value with a value in range [0,1].",
"classes": []
},
{
"type": "Segmentation",
"label": "Segmentation of pancreas related tissues. These segmentation classes were not thoroughly validated, use them on your own risk!",
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"classes": [
"veins",
"arteries",
"pancreas",
"pancreatic duct",
"bile duct"
]
}
],
"model": {
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