xcp_d.utils.plotting.plot_fmri_es

xcp_d.utils.plotting.plot_fmri_es(preprocessed_bold, uncensored_denoised_bold, interpolated_filtered_bold, TR, filtered_motion, preprocessed_bold_figure, denoised_bold_figure, standardize, mask=None, seg_data=None, run_index=None)[source]

Generate carpet plot with DVARS, FD, and WB for the executive summary.

Parameters:

  • preprocessed_bold (str) – Preprocessed BOLD file, dummy scan removal.

  • 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.

  • 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.

  • TR (float) – Repetition time of the BOLD run, in seconds.

  • filtered_motion (str) – Framewise displacement timeseries, potentially after bandstop or low-pass filtering. This is a TSV file with one column: ‘framewise_displacement’.

  • preprocessed_bold_figure (str) – output file svg before processing

  • denoised_bold_figure (str) – output file svg after processing

  • standardize (bool) – Whether to standardize the data or not. If False, then the preferred DCAN version of the plot will be generated, where the BOLD data are not rescaled, and the carpet plot has color limits of -600 and 600. If True, then the BOLD data will be z-scored and the color limits will be -2 and 2.

  • mask (str, optional) – Brain mask file. Used only when the pre- and post-processed BOLD data are NIFTIs.

  • seg_data (str, optional) – Three-tissue segmentation file. This is only used for NIFTI inputs. With CIFTI inputs, the tissue types are inferred directly from the CIFTI file.

  • run_index (None or array_like, optional) – An index indicating splits between runs, for concatenated data. If not None, this should be an array/list of integers, indicating the volumes.