Commit 3b53311d authored by Wenqi Li's avatar Wenqi Li

brain parcellation model

parent e5089e9d
[config]
version = 1.0
[download]
url = http://cmic.cs.ucl.ac.uk/platform/niftynetexamples/OASIS.tar.gz
[data]
url = http://cmic.cs.ucl.ac.uk/platform/niftynetexamples/OASIS.tar.gz?dl=1
action = expand
destination = data
[config]
version = 1.0
[download]
url = http://cmic.cs.ucl.ac.uk/platform/niftynetexamples/brain_parcellation.tar.gz
action = expand
destination = examples
......@@ -33,7 +33,7 @@ Make sure that the model directory (`~/niftynet/models/` by default) is on the `
Generate segmentations for the included example image with the command
```bash
net_segment inference -c ~/niftynet/niftynetext/dense_vnet_abdominal_ct_model_zoo/config.ini
net_segment inference -c ~/niftynet/extensions/dense_vnet_abdominal_ct_model_zoo/config.ini
```
Replace `net_segment` with `python net_segment.py` if you cloned the NiftyNet repository.
......
[config]
version = 1.0
[data]
local_id = OASIS
url = http://cmic.cs.ucl.ac.uk/platform/niftynetexamples/OASIS.tar.gz?dl=1
action = expand
destination = data
[weights]
local_id = highres3dnet_brain_parcellation
url = https://www.dropbox.com/s/nxg2ixs9rh1p9ri/highres3dnet_brain_parcellation_weights.tar.gz?dl=1
action = expand
destination = models
[network_inference_config]
local_id = highres3dnet_brain_parcellation
url = https://www.dropbox.com/s/r2q08q1kkd534p4/highres3dnet_brain_parcellation_config.tar.gz?dl=1
action = expand
destination = extensions
\ No newline at end of file
# Automatic brain parcellation on T1 MR with a high-resolution 3D net
This page describes how to acquire and use the network described in:
Li W., Wang G., Fidon L., Ourselin S., Cardoso M.J., Vercauteren T. (2017)
On the Compactness, Efficiency, and Representation of 3D
Convolutional Networks: Brain Parcellation as a Pretext Task.
In: Information Processing in Medical Imaging. IPMI 2017
This network parcellates 160 types of structures
(including 155 neuroanatomical structures) from brain MR images.
## Downloading model zoo files
If you cloned the NiftyNet repository,
the network weights and examples data can be downloaded with the command
```bash
python net_download.py highres3dnet_brain_parcellation_model_zoo
```
\ No newline at end of file
[config]
version = 1.0
[network_inference_config]
local_id = highres3dnet_brain_parcellation
url = https://www.dropbox.com/s/r2q08q1kkd534p4/highres3dnet_brain_parcellation_config.tar.gz?dl=1
action = expand
destination = extensions
\ No newline at end of file
[config]
version = 1.0
[weights]
local_id = highres3dnet_brain_parcellation
url = https://www.dropbox.com/s/nxg2ixs9rh1p9ri/highres3dnet_brain_parcellation_weights.tar.gz?dl=1
action = expand
destination = models
\ No newline at end of file
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