Multichannel Model Support for Pre-Aligned Volumes

[CavRiley]

Overview

Adds ability for training multichannel segmentation models on pre-aligned/co-registered volumes using the local datastore. I was working based off this issue #241

I added a working implementation for the BraTS 2020 dataset with individual volumes as a reference use case.

Changes

• Added optional --input_channels argument to support multichannel model configurations
• Added optional --multi_file argument to handle multi-file volume inputs (each sample has a directory with multiple volumes)
• Added optional --multichannel argument to handle multichannel inputs (example sample has a single image with multiple volumes)

Results (BraTS 2020 — 150 epochs)

Split	Mean Dice	Tumor Core	Whole Tumor	Enhancing Tumor
Train	0.875	0.883	0.914	0.830
Val	0.858	0.872	0.890	0.826

Notes

• Tested on BraTS 2020 with 4-channel input (T1, T1ce, T2, FLAIR)
• Volumes must be pre-aligned/co-registered before use

I'd be happy to incorporate any feedback from maintainers so this could be added

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