xcp_d.workflows.bold.plotting module

Workflows for generating plots from functional data.

xcp_d.workflows.bold.plotting.init_execsummary_functional_plots_wf(preproc_nifti, t1w_available, t2w_available, mem_gb, name='execsummary_functional_plots_wf')[source]

Generate the functional figures for an executive summary.

Workflow Graph

(Source code)

Parameters:

  • preproc_nifti (str or None) – BOLD data before post-processing. A NIFTI file, not a CIFTI.

  • t1w_available (bool) – Generally True.

  • t2w_available (bool) – Generally False.

  • mem_gb (dict) – Memory size in GB.

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

Inputs:

  • preproc_nifti – BOLD data before post-processing. A NIFTI file, not a CIFTI. Set from the parameter.

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

  • t1w – T1w image in a standard space, taken from the output of init_postprocess_anat_wf.

  • t2w – T2w image in a standard space, taken from the output of init_postprocess_anat_wf.

xcp_d.workflows.bold.plotting.init_qc_report_wf(TR, head_radius, name='qc_report_wf')[source]

Generate quality control figures and a QC file.

Workflow Graph
../_images/xcp_d-workflows-bold-plotting-2.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.

  • 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.

  • 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 abcc_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 – Path to the BOLD run’s brain mask in the same space as preprocessed_bold. Only used with non-CIFTI data.

  • anat_brainmask – Path to the anatomical brain mask in the same standard space as bold_mask. 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.

  • motion_file

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

Outputs:

qc_file