Faimed3d - fastai extension for volumetric medical data

Hi all,

I work as a radiologist and used fastai for some research projects. Although fastai now supports medical images, I found that it is still very challenging to apply it to 3d data, such as CT or MRI datasets. So, over the last months I wrote faimed3d, an extension to fastai, which facilitates working with 3d data.
Currently, it is possible to train 3d ResNets and 3d U-Nets using the library. It supports a variety of medical formats including DICOM, DICOM series, NIfTI and more.
I already used the library in some of my research projects and aim to further improve the functionality.
You find the GitHub repository at https://github.com/kbressem/faimed3d and the docs at https://kbressem.github.io/faimed3d/ .
I would be happy about any feedback.


This is really cool, what would be great is a tutorial notebook (maybe something from your research projects if you can share) . I had also started experimenting on extensions to the fastai.medical module but not tailored to 3D here

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I provide two example on GitHub. They are on classification using the Stanford MR-NET dataset and on segmentation using the Coronacases dataset. Examples for 4D data will come soon.

I’ll also check out you extension, it look very nice.

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Thanks!, I see the examples now, cheers for sharing this.