xcp_d.workflows.outputs.init_postproc_derivatives_wf

xcp_d.workflows.outputs.init_postproc_derivatives_wf(name_source, source_metadata, fmri_dir, bandpass_filter, low_pass, high_pass, bpf_order, fd_thresh, motion_filter_type, smoothing, params, exact_scans, cifti, dcan_qc, output_dir, custom_confounds_file, name='postproc_derivatives_wf')[source]

Write out the xcp_d derivatives in BIDS format.

Workflow Graph
../_images/xcp_d-workflows-outputs-init_postproc_derivatives_wf-1.png

(Source code, png, svg, pdf)

Parameters:

  • name_source (str) – bold or cifti files

  • source_metadata (dict)

  • fmri_dir (str) – Path to the preprocessing derivatives.

  • low_pass (float) – low pass filter

  • high_pass (float) – high pass filter

  • bpf_order

  • fd_thresh (float) – Framewise displacement threshold for censoring, in millimeters. Any framewise displacement values higher than the threshold are flagged as “high motion”. If set to <=0, no censoring will be performed. Default is 0.2 mm.

  • motion_filter_type ({None, “lp”, “notch”}) – Type of filter to use for removing respiratory artifact from motion regressors.

    If None, no filter will be applied.

    If the filter type is set to “notch”, frequencies between band_stop_min and band_stop_max will be removed with a notch filter. In this case, both band_stop_min and band_stop_max must be defined.

    If “lp”, frequencies above band_stop_min will be removed with a Butterworth filter. In this case, only band_stop_min must be defined.

  • smoothing (float) – The full width at half maximum (FWHM), in millimeters, of the Gaussian smoothing kernel that will be applied to the post-processed and denoised data. ALFF and ReHo outputs will also be smoothing with this kernel.

  • params ({“36P”, “24P”, “27P”, “acompcor”, “acompcor_gsr”, “aroma”, “aroma_gsr”, “custom”}, optional) – Shorthand for the parameter set to extract from the confounds TSV. Default is “36P”, most expansive option.

  • exact_scans (list of int, 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.

  • 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.

  • output_dir (str) – output directory

  • custom_confounds_file – Only used for Sources metadata.

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

Inputs:

  • atlas_names (list of str) – A list of atlases used for parcellating the BOLD data. The list of atlas names is generated by xcp_d.utils.atlas.get_atlas_names(). The atlases include: “4S156Parcels”, “4S256Parcels”, “4S356Parcels”, “4S456Parcels”, “4S556Parcels”, “4S656Parcels”, “4S756Parcels”, “4S856Parcels”, “4S956Parcels”, “4S1056Parcels”, “Glasser”, “Gordon”, “Tian”, and “HCP”. Used for indexing timeseries and correlations.

  • atlas_files

  • timeseries (list of str) – List of paths to atlas-specific time series TSV files. These time series are produced from the censored_denoised_bold outputs.

  • correlations (list of str) – List of paths to atlas-specific ROI-to-ROI correlation TSV files. These correlations are produced from the timeseries outputs.

  • coverage (list of str) – List of paths to atlas-specific coverage TSV files.

  • timeseries_ciftis (list of str) – List of paths to atlas-specific time series CIFTI (ptseries) files. These time series are produced from the censored_denoised_bold outputs.

  • correlation_ciftis (list of str) – List of paths to atlas-specific ROI-to-ROI correlation CIFTI (pconn) files. These correlations are produced from the timeseries_cifti outputs.

  • coverage_ciftis (list of str) – List of paths to atlas-specific coverage CIFTI (pscalar) files.

  • qc_file – LINC-style quality control file

  • 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.

  • 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.

  • alff – alff nifti

  • parcellated_alff

  • smoothed_alff – smoothed alff

  • reho

  • parcellated_reho

  • confounds_file

  • confounds_metadata

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

  • motion_metadata

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

  • temporal_mask_metadata

  • 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.