xcp_d.workflows.bold.concatenation module

Workflows for concatenating postprocessed data.

xcp_d.workflows.bold.concatenation.init_concatenate_data_wf(TR, head_radius, exact_scans, mem_gb, name='concatenate_data_wf')[source]

Concatenate postprocessed data across runs and directions.

Workflow Graph
../_images/xcp_d-workflows-bold-concatenation-1.png

(Source code, png, svg, pdf)

Parameters:

  • TR (float) – Repetition time of the BOLD run, in seconds.

  • head_radius (float or “auto”) – Radius of the head, in millimeters, for framewise displacement calculation.

    xcp_d’s default head radius is 50. The recommended value for infants is 35. A value of ‘auto’ is also supported, in which case the brain radius is estimated from the preprocessed brain mask.

  • exact_scans (list of int) – List of exact scan counts for which to compute correlation matrices from the concatenated temporal mask.

  • mem_gb (dict) – Dictionary of memory allocations with keys 'bold' and 'volume'. This should represent the total memory across all runs being concatenated.

  • name (str, optional) – Name of the workflow. This is used for working directories and workflow graphs. Default is “concatenate_data_wf”.

Inputs:

  • name_source (str) – Path to the file that will be used as the source_file for derivatives. This is generally the preprocessed BOLD file. This file does not need to exist (e.g., in the case of a concatenated version of the filename). One list entry for each run. These are used as the bases for concatenated output filenames.

  • preprocessed_bold (list of str) – The preprocessed BOLD files, after dummy volume removal.

  • motion_file – One list entry for each run.

  • temporal_mask (str) – Temporal mask; all values above fd_thresh set to 1. This is a TSV file with one column: ‘framewise_displacement’. One list entry for each run.

  • denoised_interpolated_bold (str) – Path to the censored, denoised, interpolated, and filtered BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation and band-pass filtering.

    This output should not be used for analysis. It is primarily for DCAN QC plots. One list entry for each run.

  • censored_denoised_bold (str) – Path to the censored, denoised, interpolated, filtered, and re-censored BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation, band-pass filtering, and re-censoring.

    This output is the primary derivative for analysis. One list entry for each run.

  • atlas_labels_files – Atlas labels files for each of the runs and each of the atlases.

  • bold_mask (list of str or Undefined) – Brain mask files for each of the BOLD runs. This will be a list of paths for NIFTI inputs, or a list of Undefineds for CIFTI ones.

  • anat_brainmask (str) – Anatomically-derived brain mask in the same standard space as the BOLD mask.

  • template_to_anat_xfm (str) – Path to the MNI-to-T1w transform file. May be “identity”, for testing purposes.

  • boldref (str) – Path to the BOLD reference file associated with the target BOLD run. This comes from the preprocessing derivatives.

  • timeseries (list of str) – List of paths to atlas-specific time series TSV files. These time series are produced from the censored_denoised_bold outputs. This will be a list of lists, with one sublist for each run.

  • timeseries_ciftis (list of str) – List of paths to atlas-specific time series CIFTI (ptseries) files. These time series are produced from the censored_denoised_bold outputs. This will be a list of lists, with one sublist for each run.