xcp_d.interfaces.concatenation.ConcatenateInputs

class xcp_d.interfaces.concatenation.ConcatenateInputs(from_file=None, resource_monitor=None, **inputs)[source]

Concatenate inputs.

Mandatory Inputs:

  • censored_denoised_bold (a list of items which are a pathlike object or string representing an existing file) – Denoised BOLD data.

  • filtered_motion (a list of items which are a pathlike object or string representing an existing file) – TSV files with filtered motion parameters, used for FD calculation.

  • fmriprep_confounds_file (a list of items which are a pathlike object or string representing an existing file) – TSV files with fMRIPrep confounds for individual BOLD runs.

  • interpolated_filtered_bold (a list of items which are a pathlike object or string representing an existing file) – Denoised BOLD data.

  • preprocessed_bold (a list of items which are a pathlike object or string representing an existing file) – Preprocessed BOLD files, after dummy volume removal.

  • temporal_mask (a list of items which are a pathlike object or string representing an existing file) – TSV files with high-motion outliers indexed.

  • uncensored_denoised_bold (a list of items which are a pathlike object or string representing an existing file) – Denoised BOLD data.

Optional Inputs:

  • smoothed_denoised_bold (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – Smoothed, denoised BOLD data. Optional.

  • timeseries (a list of items which are a list of items which are a pathlike object or string representing an existing file) – List of lists of parcellated time series TSV files.

  • timeseries_ciftis (a list of items which are a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – List of lists of parcellated time series CIFTI files. Only defined for CIFTI processing.

Outputs:

  • censored_denoised_bold (a pathlike object or string representing an existing file) – Concatenated denoised BOLD data.

  • filtered_motion (a pathlike object or string representing an existing file) – Concatenated TSV file with filtered motion parameters, used for FD calculation.

  • fmriprep_confounds_file (a pathlike object or string representing an existing file) – Concatenated TSV file with fMRIPrep confounds.

  • interpolated_filtered_bold (a pathlike object or string representing an existing file) – Concatenated denoised BOLD data.

  • preprocessed_bold (a pathlike object or string representing an existing file) – Concatenated preprocessed BOLD file.

  • run_index (a list of items which are an integer) – Index of join points between the uncensored runs.

  • smoothed_denoised_bold (a pathlike object or string representing an existing file or a _Undefined or None) – Concatenated, smoothed, denoised BOLD data. Optional.

  • temporal_mask (a pathlike object or string representing an existing file) – Concatenated TSV file with high-motion outliers indexed.

  • timeseries (a list of items which are a pathlike object or string representing an existing file) – Concatenated list of parcellated time series TSV files.

  • timeseries_ciftis (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – Concatenated list of parcellated time series CIFTI files. Only defined for CIFTI processing.

  • uncensored_denoised_bold (a pathlike object or string representing an existing file) – Concatenated denoised BOLD data.

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

Subclasses must implement __init__

Methods

__init__([from_file, resource_monitor])

Subclasses must implement __init__

aggregate_outputs([runtime, needed_outputs])

Collate expected outputs and apply output traits validation.

help([returnhelp])

Prints class help

load_inputs_from_json(json_file[, overwrite])

A convenient way to load pre-set inputs from a JSON file.

run([cwd, ignore_exception])

Execute this interface.

save_inputs_to_json(json_file)

A convenient way to save current inputs to a JSON file.

Attributes

always_run

Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.

can_resume

Defines if the interface can reuse partial results after interruption.

resource_monitor

version

interfaces should implement a version property