xcp_d.workflows.plotting.init_qc_report_wf

xcp_d.workflows.plotting.init_qc_report_wf(output_dir, TR, head_radius, mem_gb, omp_nthreads, cifti, dcan_qc, name='qc_report_wf')[source]

Generate quality control figures and a QC file.

Workflow Graph

(Source code)

Parameters:

  • output_dir (str) – Path to the output directory for xcp_d derivatives. This should not include the xcp_d folder. For example, “/path/to/dset/derivatives/”.

  • 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.

  • mem_gb (float) – Memory limit, in gigabytes.

  • omp_nthreads (int) – Maximum number of threads an individual process may use.

  • cifti (bool) – Post-process surface data (CIFTIs) instead of volumetric data (NIFTIs). This parameter is overridden when DCAN- or HCP-format data are provided. Default is False.

  • dcan_qc (bool) – This flag determines if DCAN-related QC steps will be taken. Enabling this flag will trigger the following steps:

    1. Brainsprite figures will be generated.

    2. The executive summary will be generated.

    3. DCAN QC files will be generated.

  • 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 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).

  • preprocessed_bold – The preprocessed BOLD file, after dummy scan removal. Used for carpet plots.

  • uncensored_denoised_bold (str) – Path to the uncensored, denoised BOLD file. This file is the result of denoising the full (uncensored) preprocessed BOLD data using betas estimated using the censored BOLD data and nuisance regressors.

    This output should not be used for analysis. It is primarily used for DCAN QC plots. Used for carpet plots. Only used if dcan_qc is True.

  • interpolated_filtered_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.

  • anat_to_native_xfm (str) – Path to the T1w-to-native BOLD space 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 above fd_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