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CMIC
NiftyNetExampleServer
Commits
6533b1ce
Commit
6533b1ce
authored
Nov 29, 2017
by
Wenqi Li
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BRATS whole tumor segmentations
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anisotropic_nets_brats_challenge_model_zoo.ini
anisotropic_nets_brats_challenge_model_zoo.ini
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anisotropic_nets_brats_challenge_model_zoo.md
anisotropic_nets_brats_challenge_model_zoo.md
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anisotropic_nets_brats_challenge_model_zoo_code.ini
anisotropic_nets_brats_challenge_model_zoo_code.ini
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anisotropic_nets_brats_challenge_model_zoo_data.ini
anisotropic_nets_brats_challenge_model_zoo_data.ini
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anisotropic_nets_brats_challenge_model_zoo_weights.ini
anisotropic_nets_brats_challenge_model_zoo_weights.ini
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model_zoo.md
model_zoo.md
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anisotropic_nets_brats_challenge_model_zoo.ini
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6533b1ce
[config]
version
=
1.0
[data]
local_id
=
BRATS_examples
url
=
https://www.dropbox.com/s/jyxnm3cqokjghje/BRATS_examples.tar.gz?dl=1
action
=
expand
destination
=
data
[weights]
local_id
=
anisotropic_nets_brats_challenge
url
=
https://www.dropbox.com/s/cnbsszxa418xc1x/anisotropic_nets_brats_challenge_weights.tar.gz?dl=1
action
=
expand
destination
=
models
[network_inference_config]
local_id
=
anisotropic_nets_brats_challenge
url
=
https://www.dropbox.com/s/fncslr3ink0jnup/anisotropic_nets_brats_challenge_code_config.tar.gz?dl=1
action
=
expand
destination
=
extensions
\ No newline at end of file
anisotropic_nets_brats_challenge_model_zoo.md
0 → 100644
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6533b1ce
# Automatic brain tumor segmentation on BRATS with anisotropic nets
This page describes how to acquire and use the whole tumor segmentation network
as a part of the pipeline described in:
Wang et al., Automatic Brain Tumor Segmentation using
Cascaded Anisotropic Convolutional Neural Networks, MICCAI BRATS 2017
[
https://arxiv.org/abs/1709.00382
](
https://arxiv.org/abs/1709.00382
)
*
[
1
]
This implementation ranked the first (in terms of averaged Dice score 0.90499) according
to the online validation leaderboard of
[
BRATS challenge 2017
](
https://www.cbica.upenn.edu/BraTS17/lboardValidation.html
)
.
*
## 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 anisotropic_nets_brats_challenge_model_zoo
```
## Generating segmentations for example data
Generate segmentations for the included example image with the command
```
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
```
Replace
`net_segment`
with
`python net_segment.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
anisotropic_nets_brats_challenge_model_zoo_code.ini
0 → 100644
View file @
6533b1ce
[config]
version
=
1.0
[network_inference_config]
local_id
=
anisotropic_nets_brats_challenge
url
=
https://www.dropbox.com/s/fncslr3ink0jnup/anisotropic_nets_brats_challenge_code_config.tar.gz?dl=1
action
=
expand
destination
=
extensions
\ No newline at end of file
anisotropic_nets_brats_challenge_model_zoo_data.ini
0 → 100644
View file @
6533b1ce
[config]
version
=
1.0
[data]
local_id
=
BRATS_examples
url
=
https://www.dropbox.com/s/jyxnm3cqokjghje/BRATS_examples.tar.gz?dl=1
action
=
expand
destination
=
data
\ No newline at end of file
anisotropic_nets_brats_challenge_model_zoo_weights.ini
0 → 100644
View file @
6533b1ce
[config]
version
=
1.0
[weights]
local_id
=
anisotropic_nets_brats_challenge
url
=
https://www.dropbox.com/s/cnbsszxa418xc1x/anisotropic_nets_brats_challenge_weights.tar.gz?dl=1
action
=
expand
destination
=
models
\ No newline at end of file
model_zoo.md
View file @
6533b1ce
...
...
@@ -7,3 +7,4 @@ This page lists NiftyNet networks pre-trained for specific tasks. Information ab
|
[
dense_vnet_abdominal_ct_model_zoo
](
./dense_vnet_abdominal_ct_model_zoo.md
)
| Segment multiple organs from abdominal CT |
|
[
ultrasound_simulator_gan_model_zoo
](
./ultrasound_simulator_gan_model_zoo.md
)
| Generate simulated ultrasound images at specified poses |
|
[
highres3dnet_brain_parcellation_model_zoo
](
./highres3dnet_brain_parcellation_model_zoo.md
)
| Brain parcellation from T1 MR images |
|
[
anisotropic_nets_brats_challenge_model_zoo
](
./anisotropic_nets_brats_challenge_model_zoo.md
)
| Brain tumor segmentation with anisotropic nets |
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