xcp_d.workflows.concatenation module
Workflows for concatenating postprocessed data.
- xcp_d.workflows.concatenation.init_concatenate_data_wf(TR, head_radius, name='concatenate_data_wf')[source]
Concatenate postprocessed data across runs and directions.
- Workflow Graph
- 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.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 thesource_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
ofstr
) – The preprocessed BOLD files, after dummy volume removal.filtered_motion (
str
) – Framewise displacement timeseries, potentially after bandstop or low-pass filtering. This is a TSV file with one column: ‘framewise_displacement’. One list entry for each run.temporal_mask (
str
) – Temporal mask; all values abovefd_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.
bold_mask (
list
ofstr
orUndefined
) – 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
)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
ofstr
) – List of paths to atlas-specific time series TSV files. These time series are produced from thecensored_denoised_bold
outputs. This will be a list of lists, with one sublist for each run.timeseries_ciftis (
list
ofstr
) – List of paths to atlas-specific time series CIFTI (ptseries) files. These time series are produced from thecensored_denoised_bold
outputs. This will be a list of lists, with one sublist for each run.