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Fixes for cli segment #73

Merged
merged 4 commits into from
Aug 31, 2023
Merged

Fixes for cli segment #73

merged 4 commits into from
Aug 31, 2023

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hasan7n
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@hasan7n hasan7n commented Aug 28, 2023

Fixes issue #(Enter issue number here)

Proposed Changes

hasan7n added 4 commits August 28, 2023 05:45
@hasan7n
rename copied tmp files as expected
2bb7b26
@hasan7n
change inference script
45b3ee9
@hasan7n
fix model weights download path
f61fb4d
@hasan7n
misc fixes
76d5a6f 
- remove `-ptd` to load inference_loader instead of trainval_loader
- rename paths for output files as expected by fusion code
@hasan7n
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hasan7n commented Aug 28, 2023

Result of running: FeTS_CLI_Segment -d /data_renamed -a fets_singlet,fets_triplet -lF STAPLE,ITKVoting,SIMPLE,MajorityVoting -g 0 -t 0:

root@3bb2af1add88:/Front-End# tree /data_renamed/
/data_renamed/
|-- BraTS-GLI-00001-001
|   |-- BraTS-GLI-00001-001_flair.nii.gz
|   |-- BraTS-GLI-00001-001_t1.nii.gz
|   |-- BraTS-GLI-00001-001_t1ce.nii.gz
|   |-- BraTS-GLI-00001-001_t2.nii.gz
|   `-- SegmentationsForQC
|       |-- BraTS-GLI-00001-001_fused_itkvoting_seg.nii.gz
|       |-- BraTS-GLI-00001-001_fused_majorityvoting_seg.nii.gz
|       |-- BraTS-GLI-00001-001_fused_simple_seg.nii.gz
|       |-- BraTS-GLI-00001-001_fused_staple_seg.nii.gz
|       |-- fets_singlet
|       |   |-- BraTS-GLI-00001-001
|       |   |   |-- BraTS-GLI-00001-001_fets_singlet_seg.nii.gz
|       |   |   `-- _t1.nii.gz
|       |   `-- _fets_singlet_subdirs_to_scores.pkl
|       |-- fets_singlet.nii.gz
|       |-- fets_triplet
|       |   |-- BraTS-GLI-00001-001
|       |   |   |-- BraTS-GLI-00001-001_fets_triplet_seg.nii.gz
|       |   |   `-- _t1.nii.gz
|       |   `-- _fets_triplet_subdirs_to_scores.pkl
|       `-- fets_triplet.nii.gz
|-- BraTS-GLI-00015-000
|   |-- BraTS-GLI-00015-000_flair.nii.gz
|   |-- BraTS-GLI-00015-000_t1.nii.gz
|   |-- BraTS-GLI-00015-000_t1ce.nii.gz
|   |-- BraTS-GLI-00015-000_t2.nii.gz
|   `-- SegmentationsForQC
|       |-- BraTS-GLI-00015-000_fused_itkvoting_seg.nii.gz
|       |-- BraTS-GLI-00015-000_fused_majorityvoting_seg.nii.gz
|       |-- BraTS-GLI-00015-000_fused_simple_seg.nii.gz
|       |-- BraTS-GLI-00015-000_fused_staple_seg.nii.gz
|       |-- fets_singlet
|       |   |-- BraTS-GLI-00015-000
|       |   |   |-- BraTS-GLI-00015-000_fets_singlet_seg.nii.gz
|       |   |   `-- _t1.nii.gz
|       |   `-- _fets_singlet_subdirs_to_scores.pkl
|       |-- fets_singlet.nii.gz
|       |-- fets_triplet
|       |   |-- BraTS-GLI-00015-000
|       |   |   |-- BraTS-GLI-00015-000_fets_triplet_seg.nii.gz
|       |   |   `-- _t1.nii.gz
|       |   `-- _fets_triplet_subdirs_to_scores.pkl
|       `-- fets_triplet.nii.gz
`-- logs

13 directories, 32 files

sarthakpati
sarthakpati approved these changes Aug 31, 2023
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LGTM

@sarthakpati sarthakpati merged commit 25eb0ca into FeTS-AI:fixing_docker_build_for_1.0 Aug 31, 2023
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@hasan7n @sarthakpati