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BAMF NNUnet Lung and Nodules (v2) #92

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BAMF NNUnet Lung and Nodules (v2) #92

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5ce512a
version 2 model for lung/nodules
jithenece Jul 9, 2024
1d77d3a
add stats
jithenece Jul 30, 2024
c9a1cfe
change folder name
jithenece Jul 30, 2024
6c1f421
add analyses to meta
jithenece Jul 30, 2024
314e4b2
update comments
jithenece Aug 8, 2024
3f6b77d
remove export map
jithenece Aug 8, 2024
cbdbbd7
fix code review comments
jithenece Aug 22, 2024
78fb580
fix meta json
jithenece Aug 22, 2024
527cd36
fix meta file
jithenece Aug 23, 2024
d6b506c
fix comments
jithenece Aug 23, 2024
f7bac4a
fix slice thickness
jithenece Aug 23, 2024
51eef5a
Merge branch 'MHubAI:main' into bamf_nnunet_ct_lung_v2
jithenece Aug 26, 2024
6d2f654
use dcm2niix engine
jithenece Aug 26, 2024
4a71c20
update model name
jithenece Aug 26, 2024
cf7536d
Merge branch 'MHubAI:main' into bamf_nnunet_ct_lung_v2
jithenece Sep 9, 2024
93b5d85
Merge branch 'MHubAI:main' into bamf_nnunet_ct_lung_v2
jithenece Sep 30, 2024
f813806
/test update test files
jithenece Sep 30, 2024
3c6f6ed
/test publication update
jithenece Oct 2, 2024
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5 changes: 4 additions & 1 deletion models/bamf_nnunet_ct_lungnodules/config/default.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,14 @@ modules:
meta:
mod: '%Modality'

NiftiConverter:
engine: dcm2niix

NNUnetRunnerV2:
in_data: nifti:mod=ct

DsegConverter:
model_name: bamf_ct_lung_nodule
model_name: bamf_nnunet_ct_lungnodules
target_dicom: dicom:mod=ct
source_segs: nifti:mod=seg:processor=bamf
skip_empty_slices: True
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2 changes: 1 addition & 1 deletion models/bamf_nnunet_ct_lungnodules/meta.json
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Expand Up @@ -11,7 +11,7 @@
"format": "DICOM",
"modality": "CT",
"bodypartexamined": "LUNG",
"slicethickness": "10mm",
"slicethickness": "3mm",
"non-contrast": true,
"contrast": false
}
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