highres3dnet_brain_parcellation_model_zoo.md 1.08 KB
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# 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)
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On the Compactness, Efficiency, and Representation of 3D
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Convolutional Networks: Brain Parcellation as a Pretext Task.
In: Information Processing in Medical Imaging. IPMI 2017

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This network parcellates 160 types of structures
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(including 155 neuroanatomical structures) from brain MR images.
## Downloading model zoo files

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The network weights and examples data can be downloaded with the command
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```bash
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net_download highres3dnet_brain_parcellation_model_zoo
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```

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(Replace `net_download` with `python net_download.py` if you cloned the NiftyNet repository.)

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## Generating segmentations for example data

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Generate segmentations for the included example image with the command
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```bash
net_segment inference -c ~/niftynet/extensions/highres3dnet_brain_parcellation/highres3dnet_config_eval.ini
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```

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Replace `net_segment` with `python net_segment.py` if you cloned the NiftyNet repository.