OpenNeuro App Highlights: MAGeT-Brain

October 2, 2017

This is a first episode of a series of blog posts highlighting image analysis apps available on the platform. This piece was contributed by Gabriel A. Devenyi and Mallar Chakravarty.

New to the OpenNeuro platform is the automatic structural segmentation pipeline MAGeT-Brain. Coming along with the pipeline are 5 expertly-segmented atlas/label combinations, at 0.3 mm isotropic, in T1 and T2, providing automatic segmentation of

  1. Subcortical structures: striatum, thalamus, globus pallidus
  2. Hippocampus subfields and hippocampal white matter
  3. Cerebellum and its lobules
  4. Amygdala


Figure 1: Example subcortical segmentation

MAGeT-Brain is an extension of the classic registration based “multi-atlas” segmentation method, where labels on manually segmented atlases are transformed via linear/non-linear registration onto a set of subjects. The resulting candidate segmentations are combined via some label fusion technique.


Figure 2: Classical multi-atlas vs. MAGeT-Brain segmentation

The innovation of MAGeT-Brain lies in the introduction of the “template” layer, a representative subset of the subject population, which is used to increase the anatomical variance in the atlas set. These new template brains are used to produce the candidate segmentations on the subject brains, resulting in a much larger total number of candidates and overall better segmentations. Such a pipeline is relatively computationally expensive, requiring cluster computing to produce results in a reasonable amount of time. MAGeT-Brain has been validated and compared to other leading segmentation tools and found to be superior for low atlas counts, and equivalent for higher atlas counts. Since the production of high-resolution, anatomically-informed manual segmentations is very labour intensive, MAGeT-Brain’s computational load is a reasonable tradeoff to produce optimal segmentations.

Previously MAGeT-Brain was implemented to support the specialized MINC2 file format. However, this pipeline was recently rewritten to support all file formats supported by ITK and ANTs, allowing integration into BIDS-Apps and OpenNeuro via a small runtime shim.

We welcome our new users of OpenNeuro and hope you find this tool useful!


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