Spaces:
Running
Running
Fixed README regarding threshold -1 feature [no ci]
Browse files
README.md
CHANGED
|
@@ -57,11 +57,13 @@ lungtumormask input_file output_file
|
|
| 57 |
lungtumormask patient_01.nii.gz mask_01.nii.gz
|
| 58 |
|
| 59 |
# Custom arguments
|
| 60 |
-
lungtumormask patient_01.nii.gz mask_01.nii.gz --lung-filter --threshold 0.3 --radius 3 --batch-size 8 --cpu
|
| 61 |
```
|
| 62 |
|
| 63 |
In the last example, we filter tumor candidates outside the lungs, use a lower probability threshold to boost recall, use a morphological smoothing step
|
| 64 |
-
to fill holes inside segmentations using a disk kernel of radius 3, `--cpu` to disable the GPU during computation
|
|
|
|
|
|
|
| 65 |
|
| 66 |
## [Applications](https://github.com/VemundFredriksen/LungTumorMask#applications)
|
| 67 |
* The software has been successfully integrated into the open platform [Fraxinus](https://github.com/SINTEFMedtek/Fraxinus).
|
|
|
|
| 57 |
lungtumormask patient_01.nii.gz mask_01.nii.gz
|
| 58 |
|
| 59 |
# Custom arguments
|
| 60 |
+
lungtumormask patient_01.nii.gz mask_01.nii.gz --lung-filter --threshold 0.3 --radius 3 --batch-size 8 --cpu
|
| 61 |
```
|
| 62 |
|
| 63 |
In the last example, we filter tumor candidates outside the lungs, use a lower probability threshold to boost recall, use a morphological smoothing step
|
| 64 |
+
to fill holes inside segmentations using a disk kernel of radius 3, and `--cpu` to disable the GPU during computation.
|
| 65 |
+
|
| 66 |
+
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.
|
| 67 |
|
| 68 |
## [Applications](https://github.com/VemundFredriksen/LungTumorMask#applications)
|
| 69 |
* The software has been successfully integrated into the open platform [Fraxinus](https://github.com/SINTEFMedtek/Fraxinus).
|