ENH: Minimize clipping prior to surface reconstruction with MCRIBS #436
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For FreeSurfer / InfantFS, we have passed in the anatomical template - not the preprocessed anatomical - as the input. However, MCRIBS is different, since we are bypassing some of the early preprocessing in the pipeline (conforming, n4, etc). However, due to the intensity clipping, it was reported that the white matter white surface may have been hitting the upper bounds, potentially leading to a decrease in cortical thickness.
This PR restructures the MCRIBS pipeline in the following ways:
rescale_intensities
to actually run (it is disabled without a mask present).