aslprep.interfaces.utility module

Utility interfaces for ASLPrep.

class CombineMotionParameters(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Combine motion parameter files from MCFLIRT across image types.

Optional Inputs:

  • aslcontext (a pathlike object or string representing an existing file)

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

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

  • volume_types (a list of items which are a string)

Outputs:

  • combined_par_file (a pathlike object or string representing an existing file)

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

class PairwiseRMSDiff(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Run rmsdiff on each contiguous pair of transform files to build a txt file of rmsd values.

This interface uses RMSDiff internally, which may not be a proper nipype pattern.

Mandatory Inputs:

  • in_files (a list of items which are a pathlike object or string representing an existing file) – Matrix files to compare with each other.

  • ref_file (a pathlike object or string representing an existing file) – Reference volume.

Outputs:

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

class RMSDiff(**inputs)[source]

Bases: FSLCommand

Wrapped executable: rmsdiff.

Run rmsdiff.

Mandatory Inputs:

  • matrixfile1 (a pathlike object or string representing an existing file) – First matrix file. Maps to a command-line argument: %s (position: 0).

  • matrixfile2 (a pathlike object or string representing an existing file) – Second matrix file. Maps to a command-line argument: %s (position: 1).

  • ref_vol (a pathlike object or string representing an existing file) – Reference volume. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.

Outputs:

rmsd (a float)

aggregate_outputs(runtime=None, needed_outputs=None)[source]

Taken from nipype.interfaces.afni.preprocess.ClipLevel.

class ReduceASLFiles(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Split ASL data into different files.

Mandatory Inputs:

  • asl_file (a pathlike object or string representing an existing file) – ASL file to split.

  • aslcontext (a pathlike object or string representing an existing file) – Aslcontext TSV.

Optional Inputs:

  • metadata (a dictionary with keys which are any value and with values which are any value)

  • processing_target (a string)

Outputs:

  • asl_file (a pathlike object or string representing an existing file) – Modified ASL file.

  • aslcontext (a pathlike object or string representing an existing file) – Modified aslcontext file.

  • metadata (a dictionary with keys which are any value and with values which are any value)

class Smooth(check_import=True, *args, **kwargs)[source]

Bases: NilearnBaseInterface, SimpleInterface

Smooth image.

Mandatory Inputs:

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

Optional Inputs:

  • fwhm (a float or a list of from 3 to 3 items which are a float) – Full width at half maximum. Smoothing strength, as a full-width at half maximum, in millimeters.

  • out_file (a pathlike object or string representing a file) – The name of the smoothed file to write out. smooth_img.nii.gz by default. (Nipype default value: smooth_img.nii.gz)

Outputs:

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

class SplitByVolumeType(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Split out a specific volume type from the ASL file.

Optional Inputs:

  • asl_file (a pathlike object or string representing an existing file)

  • aslcontext (a pathlike object or string representing an existing file)

Outputs:

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

  • volume_types (a list of items which are a string)