torchio 0.16.9

Tools for loading, augmenting and writing 3D medical images on PyTorch.

TorchIO

Tools like TorchIO are a symptom of the maturation of medical AI research using deep learning techniques.

Jack Clark, Policy Director at OpenAI (link).

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Original	Random blur
Random flip	Random noise
Random affine transformation	Random elastic transformation
Random bias field artifact	Random motion artifact
Random spike artifact	Random ghosting artifact

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(Queue for patch-based training)

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TorchIO is a Python package containing a set of tools to efficiently read, preprocess, sample, augment, and write 3D medical images in deep learning applications written in PyTorch, including intensity and spatial transforms for data augmentation and preprocessing. Transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity or k-space motion artifacts.

This package has been greatly inspired by NiftyNet, which is not actively maintained anymore.

Documentation

The documentation is hosted on Read the Docs.

Please create a new issue if you think something is missing.

Credits

If you like this repository, please click on Star!

If you use this package for your research, please cite the paper:

Pérez-García et al., 2020, TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning.

BibTeX entry:

@misc{fern2020torchio,
    title={TorchIO: a Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning},
    author={Fernando Pérez-García and Rachel Sparks and Sebastien Ourselin},
    year={2020},
    eprint={2003.04696},
    archivePrefix={arXiv},
    primaryClass={eess.IV}
}

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Fernando Pérez-García 💻 📖	valabregue 🤔 👀 💻	GFabien 💻	G.Reguig 💻	Niels Schurink 💻	Ibrahim Hadzic 🐛	ReubenDo 🤔
Julian Klug 🤔	David Völgyes 🤔	Jean-Christophe Fillion-Robin 📖	Suraj Pai 🤔	Ben Darwin 🤔

This project follows the all-contributors specification. Contributions of any kind welcome!

History

0.15.0 (07-04-2020)

• Refactor RandomElasticDeformation transform
• Make Subject inherit from dict

0.14.0 (31-03-2020)

• Add datasets module
• Add support for DICOM files
• Add documentation
• Add CropOrPad transform

0.13.0 (24-02-2020)

• Add Subject class
• Add random blur transform
• Add lambda transform
• Add random patches swapping transform
• Add MRI k-space ghosting artefact augmentation

0.12.0 (21-01-2020)

• Add ToCanonical transform
• Add CenterCropOrPad transform

0.11.0 (15-01-2020)

• Add Resample transform

0.10.0 (15-01-2020)

• Add Pad transform
• Add Crop transform

0.9.0 (14-01-2020)

• Add CLI tool to transform an image from file

0.8.0 (11-01-2020)

• Add Image class

0.7.0 (02-01-2020)

• Make transforms use PyTorch tensors consistently

0.6.0 (02-01-2020)

• Add support for NRRD

0.5.0 (01-01-2020)

• Add bias field transform

0.4.0 (29-12-2019)

• Add MRI k-space motion artefact augmentation

0.3.0 (21-12-2019)

• Add Rescale transform
• Add support for multimodal data and missing modalities

0.2.0 (2019-12-06)

• First release on PyPI.