xcp_d.interfaces.concatenation module

Interfaces for the concatenation workflow.

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

Bases: SimpleInterface

Remove run entity from the name source.

Mandatory Inputs:

name_source (a list of items which are a pathlike object or string representing an existing file) – Name source files.

Outputs:

name_source (a string) – Name source.

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

Bases: SimpleInterface

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.

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

Bases: SimpleInterface

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.