sdcflows.interfaces.brainmask module

Brain extraction interfaces.

class sdcflows.interfaces.brainmask.BinaryDilation(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Brain extraction for EPI and GRE data.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Binary file to dilate.

Optional Inputs:

radius (a float) – Structure element (ball) radius. (Nipype default value: 3)

Outputs:

out_file (a pathlike object or string representing an existing file) – The input file, after binary dilation.

class sdcflows.interfaces.brainmask.BrainExtraction(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Brain extraction for EPI and GRE data.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – File to mask.

Outputs:

  • out_file (a pathlike object or string representing an existing file) – The input file, after masking.

  • out_mask (a pathlike object or string representing an existing file) – The binary brain mask.

  • out_probseg (a pathlike object or string representing an existing file) – The probabilistic brain mask.

class sdcflows.interfaces.brainmask.Union(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Brain extraction for EPI and GRE data.

Mandatory Inputs:

  • in1 (a pathlike object or string representing an existing file) – Binary file.

  • in2 (a pathlike object or string representing an existing file) – Binary file.

Outputs:

out_file (a pathlike object or string representing an existing file) – The input file, after binary dilation.