Skip to main content

PyTorch implementation of HighResNet

Project description

HighRes3DNet

License: MIT PyPI version DOI

$ NII_FILE=`download_oasis`
$ deepgif $NII_FILE

3D Slicer screenshot

PyTorch implementation of HighRes3DNet from Li et al. 2017, On the Compactness, Efficiency, and Representation of 3D Convolutional Networks: Brain Parcellation as a Pretext Task.

All the information about how the weights were ported from NiftyNet can be found in my submission to the MICCAI Educational Challenge 2019.

A 2D version (HighRes2DNet) is also available.

Usage

Command line interface

(deepgif) $ deepgif t1_mri.nii.gz
Using cache found in /home/fernando/.cache/torch/hub/fepegar_highresnet_master
100%|███████████████████████████████████████████| 36/36 [01:13<00:00,  2.05s/it]

PyTorch Hub

If you are using pytorch>=1.2.0, you can import the model directly from this repository using PyTorch Hub.

>>> import torch
>>> repo = 'fepegar/highresnet'
>>> model_name = 'highres3dnet'
>>> print(torch.hub.help(repo, model_name))

        "HighRes3DNet by Li et al. 2017 for T1-MRI brain parcellation"
        "pretrained (bool): load parameters from pretrained model"

>>> model = torch.hub.load(repo, model_name, pretrained=True)

Installation

1. Create a conda environment (recommended)

ENVNAME="gifenv"
conda create -n $ENVNAME python -y
conda activate $ENVNAME

2. Install PyTorch and highresnet

Within the conda environment:

pip install pytorch highresnet

Now you can do

>>> from highresnet import HighRes3DNet
>>> model = HighRes3DNet(in_channels=1, out_channels=160)
>>>

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

highresnet-0.6.1.tar.gz (10.5 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page