xcp_d.interfaces.concatenation.FilterOutFailedRuns

class xcp_d.interfaces.concatenation.FilterOutFailedRuns(from_file=None, resource_monitor=None, **inputs)

Reduce several input lists based on whether entries in one list are defined or not.

Mandatory Inputs:

• atlas_names (a list of items which are a list of items which are a string) – List of lists of atlas names, corresponding to timeseries and timeseries_ciftis.

• censored_denoised_bold (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – Denoised BOLD data. This is used to index successful runs.

• filtered_motion (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – 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 or a _Undefined or None) – 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 or a _Undefined or None) – Denoised BOLD data.

• preprocessed_bold (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – Preprocessed BOLD files, after dummy volume removal.

• temporal_mask (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – TSV files with high-motion outliers indexed.

• 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.

• uncensored_denoised_bold (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – Denoised BOLD data.

Optional Inputs:

• anat_to_native_xfm (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – T1w-to-native space transform files. Only used for NIFTI processing.

• bold_mask (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – BOLD-based brain mask file. Only used for NIFTI processing.

• boldref (a list of items which are a pathlike object or string representing an existing file or a _Undefined or None) – BOLD reference files. Only used for NIFTI processing.

• 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. Only set if smoothing was done in postprocessing.

• 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:

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

• atlas_names (a list of items which are a list of items which are a string) – List of lists of atlas names, corresponding to timeseries and timeseries_ciftis.

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

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

• 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) – FMRIPrep confounds files, after dummy volume removal.

• 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.

• 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.

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

• 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.

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

__init__(from_file=None, resource_monitor=None, **inputs)

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