sdcflows.workflows.ancillary module#

Estimate fieldmaps for SDC.

sdcflows.workflows.ancillary.init_brainextraction_wf(name='brainextraction_wf')[source]#

Remove nonbrain tissue from images.

Parameters:

name (str, optional) – Workflow name (default: "brainextraction_wf")

Inputs:

  • in_file (str) – the GRE magnitude or EPI reference to be brain-extracted

  • bspline_dist (int, optional) – Integer to replace default distance of b-spline separation for N4

Outputs:

  • out_file (str) – the input file after N4 and smart clipping

  • out_brain (str) – the output file, just the brain extracted

  • out_mask (str) – the calculated mask

  • out_probseg (str) – a probability map that the random walker reached a given voxel (some sort of “soft” brainmask)