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Fixed README regarding threshold -1 feature [no ci]
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README.md
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@@ -57,11 +57,13 @@ lungtumormask input_file output_file
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lungtumormask patient_01.nii.gz mask_01.nii.gz
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# Custom arguments
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lungtumormask patient_01.nii.gz mask_01.nii.gz --lung-filter --threshold 0.3 --radius 3 --batch-size 8 --cpu
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```
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In the last example, we filter tumor candidates outside the lungs, use a lower probability threshold to boost recall, use a morphological smoothing step
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to fill holes inside segmentations using a disk kernel of radius 3, `--cpu` to disable the GPU during computation
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## [Applications](https://github.com/VemundFredriksen/LungTumorMask#applications)
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* The software has been successfully integrated into the open platform [Fraxinus](https://github.com/SINTEFMedtek/Fraxinus).
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lungtumormask patient_01.nii.gz mask_01.nii.gz
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# Custom arguments
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lungtumormask patient_01.nii.gz mask_01.nii.gz --lung-filter --threshold 0.3 --radius 3 --batch-size 8 --cpu
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```
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In the last example, we filter tumor candidates outside the lungs, use a lower probability threshold to boost recall, use a morphological smoothing step
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to fill holes inside segmentations using a disk kernel of radius 3, and `--cpu` to disable the GPU during computation.
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You can also output the raw probability map (without any post-processing), by setting `--threshold -1` instead. By default a threshold of 0.5 is used.
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## [Applications](https://github.com/VemundFredriksen/LungTumorMask#applications)
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* The software has been successfully integrated into the open platform [Fraxinus](https://github.com/SINTEFMedtek/Fraxinus).
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