qsiprep.interfaces.confounds module

Handling confounds

>>> import os
>>> import pandas as pd
class qsiprep.interfaces.confounds.DMRISummary(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Optional Inputs:

  • bval_files (a list of items which are a pathlike object or string representing an existing file) – Bvals files.

  • confounds_file (a pathlike object or string representing an existing file) – BIDS’ _desc-confounds_timeseries.tsv file.

  • confounds_list (a list of at least 1 items which are a string or a tuple of the form: (a string, a string or None) or a tuple of the form: (a string, a string or None, a string or None)) – List of headers to extract from the confounds_file.

  • orig_bvecs (a list of items which are a pathlike object or string representing an existing file) – Original bvecs file.

  • sliceqc_file (a pathlike object or string representing an existing file) – Output from SliceQC.

  • sliceqc_mask (a pathlike object or string representing an existing file) – Mask.

  • str_or_tuple (a string or a tuple of the form: (a string, a string or None) or a tuple of the form: (a string, a string or None, a string or None))

Outputs:

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

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

class qsiprep.interfaces.confounds.GatherConfounds(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Combine various sources of confounds in one TSV file

Optional Inputs:

  • denoising_confounds (a pathlike object or string representing an existing file) – Descriptive statistics from denoising.

  • fd (a pathlike object or string representing an existing file) – Input framewise displacement.

  • motion (a pathlike object or string representing an existing file) – Input motion parameters.

  • original_bvals (a list of items which are a pathlike object or string representing an existing file) – Originals bval files.

  • original_bvecs (a list of items which are a pathlike object or string representing an existing file) – Original bvec files.

  • original_files (a list of items which are any value) – Original grouping of each volume.

  • sliceqc_file (a pathlike object or string representing an existing file) – Output from sliceqc.

Outputs:

  • confounds_file (a pathlike object or string representing an existing file) – Output confounds file.

  • confounds_list (a list of items which are a string) – List of headers.