xcp_d.workflows.cifti module
Workflows for post-processing CIFTI-format BOLD data.
- xcp_d.workflows.cifti.init_postprocess_cifti_wf(bold_file, head_radius, run_data, t1w_available, t2w_available, n_runs, exact_scans, name='cifti_postprocess_wf')[source]
Organize the cifti processing workflow.
- Workflow Graph
- Parameters:
bold_file
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. This will already be estimated before this workflow.run_data (dict)
t1w_available
t2w_available
n_runs – Number of runs being postprocessed by XCP-D. This is just used for the boilerplate, as this workflow only posprocesses one run.
exact_scans (
list
ofint
, optional) – If used, this parameter will produce correlation matrices limited to each requested amount of time. If there is more than the required amount of low-motion data, then volumes will be randomly selected to produce denoised outputs with the exact amounts of time requested. If there is less than the required amount of ‘good’ data, then the run will not be post-processed.name (
str
, optional) – Name of the workflow. This is used for working directories and workflow graphs. Default is “cifti_postprocess_wf”.
- Inputs:
bold_file – CIFTI file
boldref (
str
) – Path to the BOLD reference file associated with the target BOLD run. This comes from the preprocessing derivatives.custom_confounds_file (
str
or None) – Path to custom nuisance regressors.t1w – Preprocessed T1w image, warped to standard space. Fed from the subject workflow.
t2w – Preprocessed T2w image, warped to standard space. Fed from the subject workflow.
fmriprep_confounds_file (
str
) – Confounds TSV file from preprocessing derivatives.fmriprep_confounds_json
dummy_scans (
int
or “auto”) – Number of volumes to remove from the beginning of each run. If set to ‘auto’, xcp_d will extract non-steady-state volume indices from the preprocessing derivatives’ confounds file.
- Outputs:
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).preprocessed_bold (
str
) – The preprocessed BOLD file, after dummy scan removal.fmriprep_confounds_file (
str
) – Confounds TSV file from preprocessing derivatives. After dummy scan removal.filtered_motion (
str
) – Framewise displacement timeseries, potentially after bandstop or low-pass filtering. This is a TSV file with one column: ‘framewise_displacement’.temporal_mask (
str
) – Temporal mask; all values abovefd_thresh
set to 1. This is a TSV file with one column: ‘framewise_displacement’.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.
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.
smoothed_denoised_bold (
str
) – Path to the censored, denoised, interpolated, filtered, re-censored, and smoothed BOLD file. This file is the result of denoising the censored preprocessed BOLD data, followed by cubic spline interpolation, band-pass filtering, re-censoring, and spatial smoothing.boldref (
str
) – Path to the BOLD reference file associated with the target BOLD run. This comes from the preprocessing derivatives.bold_mask – This will not be defined.
timeseries (
list
ofstr
) – List of paths to atlas-specific time series TSV files. These time series are produced from thecensored_denoised_bold
outputs.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.
References