[FEATURE REQUEST] Add option to provide external segmentation maps

schorschinho / osprey

All-in-one toolbox for processing of magnetic resonance spectroscopy data.

https://schorschinho.github.io/osprey

MIT License

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[FEATURE REQUEST] Add option to provide external segmentation maps #396

Closed schorschinho closed 2 years ago

schorschinho commented 2 years ago

Is your feature request related to a problem? Please describe. Osprey currently calls SPM to perform segmentation of structural anatomical images, but there is no way to provide pre-segmented tissue class maps instead (e.g. produced by deep-learning methods specifically designed for certain cohorts).

Describe the solution you'd like Add fields to the job file that provide a pathway for supplying pre-segmented tissue class maps.

HJZollner commented 2 years ago

External segmentation maps are supported with #409 . Still need to be tested with the implementation provided in the HBCD study.

HJZollner commented 2 years ago

External segmentation is supported for different formats these include:

external probability maps for tissue types (separate 3D volumes or single 4D volume)
external label maps with binarized results (theses have to be changed manually according to the atlas/lableing convention)