Commit c58e843b authored by Wenqi Li's avatar Wenqi Li

Merge branch 'revising-config' into 'master'

adding averaging script

See merge request !6
parents a3d5bb18 5270d9a4
......@@ -13,7 +13,7 @@ to the online validation leaderboard of [BRATS challenge 2017](https://www.cbica
## Downloading model zoo files
If you cloned the NiftyNet repository,
If you cloned the NiftyNet repository,
the network weights and examples data can be downloaded with the command
```bash
python net_download.py anisotropic_nets_brats_challenge_model_zoo
......@@ -21,13 +21,31 @@ python net_download.py anisotropic_nets_brats_challenge_model_zoo
## Generating segmentations for example data
Generate segmentations for the included example image with the command
Generate segmentations for the included example image with the command,
For the network operates in axial view:
```bash
net_run inference -a anisotropic_nets_brats_challenge.brats_seg_app.BRATSApp \
-c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_axial.ini
```
For the network operates in coronal view:
```bash
net_run inference -a anisotropic_nets_brats_challenge.brats_seg_app.BRATSApp \
-c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_coronal.ini
```
For the network operates in sagittal view:
```bash
net_segment inference -c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_axial.ini
net_segment inference -c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_coronal.ini
net_segment inference -c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_sagittal.ini
net_run inference -a anisotropic_nets_brats_challenge.brats_seg_app.BRATSApp \
-c ~/niftynet/extensions/anisotropic_nets_brats_challenge/whole_tumor_sagittal.ini
```
Replace `net_segment` with `python net_segment.py` if you cloned the NiftyNet repository.
Replace `net_run` with `python net_run.py` if you cloned the NiftyNet repository.
Replace `~/niftynet/` if you specified a custom download path in the `net_download` command.
\ No newline at end of file
## Generating averaged volume from the outcomes of the previous step
A script has been created to compute the averaged volumes and
the Dice coefficients from the probabilistic outputs of the segmentation step.
```bash
python ~/niftynet/extensions/anisotropic_nets_brats_challenge/average_volume.py
```
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