niworkflows.anat.skullstrip module

Brain extraction workflows.

niworkflows.anat.skullstrip.afni_wf(name='AFNISkullStripWorkflow', unifize=False, n4_nthreads=1)[source]

Create a skull-stripping workflow based on AFNI’s tools.

Originally derived from the codebase of the QAP. Now, this workflow includes INU correction using the N4 algorithm and (optionally) intensity harmonization using ANFI’s 3dUnifize.

Workflow Graph
../_images/niworkflows-anat-skullstrip-1.png

(Source code, png, svg, pdf)

Parameters:

  • n4_nthreads (int) – number of cpus N4 bias field correction can utilize.

  • unifize (bool) – whether AFNI’s 3dUnifize should be applied (default: False).

  • name (str) – name for the workflow hierarchy of Nipype

Inputs:

in_file (str) – input T1w image.

Outputs:

  • bias_corrected (str) – path to the bias corrected input MRI.

  • out_file (str) – path to the skull-stripped image.

  • out_mask (str) – path to the generated brain mask.

  • bias_image (str) – path to the B1 inhomogeneity field.