qsiprep.interfaces.itk module

ITK files handling

class qsiprep.interfaces.itk.ACPCReport(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

translation_image (a pathlike object or string representing an existing file) – Only translated to ACPC.

Optional Inputs:

rigid_image (a pathlike object or string representing an existing file) – Rigid transformed to ACPC.

Outputs:

out_report (a pathlike object or string representing an existing file)

class qsiprep.interfaces.itk.AffineToRigid(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Optional Inputs:

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

Outputs:

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

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

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

class qsiprep.interfaces.itk.DisassembleTransform(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Sloppy interface to split h5 transforms to a warp and an affine.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – ANTs composite transform (h5).

Outputs:

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

qsiprep.interfaces.itk.compose_affines(reference_image, affine_list, output_file)

Use antsApplyTransforms to get a single affine from multiple affines.

qsiprep.interfaces.itk.disassemble_transform(transform_file, cwd)

qsiprep.interfaces.itk.itk_affine_to_rigid(transform_file, cwd)

uses c3d_affine_tool and FSL’s aff2rigid to convert an itk linear transform from affine to rigid