Commit f36d41fd authored by Wenqi Li's avatar Wenqi Li

Update anisotropic_nets_brats_challenge_model_zoo.md

parent 798a8ee5
......@@ -23,6 +23,22 @@ net_download anisotropic_nets_brats_challenge_model_zoo
(Replace `net_download` with `python net_download.py` if you cloned the NiftyNet repository.)
After running this command successfully, the downloaded files include:
* `brats_seg_app.py` --
an application built with NiftyNet, defines the main workflow of network
training and inference.
* `wt_net.py` --
the network definitions.
* `.ini` files --
configuration files define system parameters for running
segmentation networks, the three files correspond to the networks in three orientations
[axial, coronal, sagittal] configurations.
* `label_mapping_whole_tumor.txt` --
mapping file used by NiftyNet, to convert the multi-class segmentations
into a binary problem.
## Generating segmentations for example data
Generate segmentations for the included example image with the command,
......@@ -54,6 +70,10 @@ A script has been created to compute the averaged volumes and
python ~/niftynet/extensions/anisotropic_nets_brats_challenge/average_volume.py
```
A script [`rename_crop_BRATS.py`](https://github.com/NifTK/NiftyNet/blob/dev/demos/BRATS17/rename_crop_BRATS.py) is also available to to rename BRATS17 images into
`TYPEindex_modality.nii.gz` format and crop with a bounding box to remove
image background (voxels with intensity value zero).
---
Example data used in this model zoo entry are taken from
......
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