xcp_d.workflows.plotting module
Plotting workflows.
- xcp_d.workflows.plotting.init_qc_report_wf(TR, head_radius, name='qc_report_wf')[source]
Generate quality control figures and a QC file.
- 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 “qc_report_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).preprocessed_bold – The preprocessed BOLD file, after dummy scan removal. Used for carpet plots.
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. Used for DCAN carpet plots. Only used if dcan_qc is True.
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. Used for LINC carpet plots.
boldref (
str
) – Path to the BOLD reference file associated with the target BOLD run. This comes from the preprocessing derivatives. Only used with non-CIFTI data.bold_mask – Only used with non-CIFTI data.
anat_brainmask – Only used with non-CIFTI data.
template_to_anat_xfm (
str
) – Path to the MNI-to-T1w transform file. May be “identity”, for testing purposes. Only used with non-CIFTI data.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.fmriprep_confounds_file (
str
) – Confounds TSV file from preprocessing derivatives.temporal_mask (
str
) – Temporal mask; all values abovefd_thresh
set to 1. This is a TSV file with one column: ‘framewise_displacement’.filtered_motion (
str
) – Framewise displacement timeseries, potentially after bandstop or low-pass filtering. This is a TSV file with one column: ‘framewise_displacement’.
- Outputs:
qc_file