niworkflows.interfaces.nibabel module#

Nibabel-based interfaces.

class niworkflows.interfaces.nibabel.ApplyMask(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Mask the input given a mask.

Mandatory Inputs

  • in_file (a pathlike object or string representing an existing file) – An image.

  • in_mask (a pathlike object or string representing an existing file) – A mask.

Optional Inputs

threshold (a float) – A threshold to the mask, if it is nonbinary. (Nipype default value: 0.5)

Outputs

out_file (a pathlike object or string representing an existing file) – Masked file.

class niworkflows.interfaces.nibabel.Binarize(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Binarizes the input image applying the given thresholds.

Mandatory Inputs

  • in_file (a pathlike object or string representing an existing file) – Input image.

  • thresh_low (a float) – Non-inclusive lower threshold.

Outputs

  • out_file (a pathlike object or string representing an existing file) – Masked file.

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

class niworkflows.interfaces.nibabel.MergeSeries(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Merge a series of 3D volumes along the last dimension into a single 4D image.

Optional Inputs

  • allow_4D (a boolean) – Whether 4D images are allowed to be concatenated. (Nipype default value: True)

  • in_files (a list of items which are a pathlike object or string representing an existing file)

Outputs

out_file (a pathlike object or string representing an existing file) – Output 4d image.

class niworkflows.interfaces.nibabel.SplitSeries(from_file=None, resource_monitor=None, **inputs)[source]#

Bases: nipype.interfaces.base.core.SimpleInterface

Split a 4D dataset along the last dimension into a series of 3D volumes.

Mandatory Inputs

in_file (a pathlike object or string representing an existing file) – Input 4d image.

Outputs

out_files (a list of items which are a pathlike object or string representing an existing file) – Output list of 3d images.