xcp_d.interfaces.censoring module

Interfaces for the post-processing workflows.

class xcp_d.interfaces.censoring.Censor(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Apply temporal mask to data.

Mandatory Inputs:

  • in_file (a pathlike object or string representing an existing file) – BOLD file after denoising, interpolation, and filtering.

  • temporal_mask (a pathlike object or string representing an existing file) – Temporal mask; all motion outlier volumes set to 1. This is a TSV file with one column: ‘framewise_displacement’.

Outputs:

  • censored_confounds (a pathlike object or string representing an existing file) – Confounds_file censored.

  • censored_denoised_bold (a pathlike object or string representing an existing file) – Censored bold file.

  • censored_motion (a pathlike object or string representing an existing file) – Framewise displacement timeseries. This is a TSV file with one column: ‘framewise_displacement’.

class xcp_d.interfaces.censoring.GenerateConfounds(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Load, consolidate, and filter confounds.

Also, generate the temporal mask.

Mandatory Inputs:

  • TR (a float) – Repetition time in seconds.

  • band_stop_max (a float or None) – Upper frequency for the band-stop motion filter, in breaths-per-minute (bpm).

  • band_stop_min (a float or None) – Lower frequency for the band-stop motion filter, in breaths-per-minute (bpm).

  • custom_confounds_file (a pathlike object or string representing an existing file or None) – Custom confounds tsv.

  • fmriprep_confounds_file (a pathlike object or string representing an existing file) – FMRIPrep confounds tsv.

  • fmriprep_confounds_json (a pathlike object or string representing an existing file) – FMRIPrep confounds json.

  • in_file (a pathlike object or string representing an existing file) – BOLD file after denoising, interpolation, and filtering.

  • motion_filter_order (an integer or None)

  • motion_filter_type (a string or None)

  • params (a string) – Parameter set for regression.

Optional Inputs:

  • fd_thresh (a float) – Framewise displacement threshold. All values above this will be dropped.

  • head_radius (a float) – Head radius in mm .

Outputs:

  • confounds_file (a pathlike object or string representing an existing file) – The selected confounds. This may include custom confounds as well. It will also always have the linear trend and a constant column.

  • filtered_confounds_file (a pathlike object or string representing an existing file) – The original fMRIPrep confounds, with the motion parameters and their Volterra expansion regressors replaced with filtered versions.

  • motion_file (a pathlike object or string representing an existing file) – The filtered motion parameters.

  • motion_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata associated with the filtered_motion output.

  • temporal_mask (a pathlike object or string representing an existing file) – Temporal mask; all values above fd_thresh set to 1. This is a TSV file with one column: ‘framewise_displacement’.

  • temporal_mask_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata associated with the temporal_mask output.

class xcp_d.interfaces.censoring.RemoveDummyVolumes(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Removes initial volumes from a nifti or cifti file.

A bold file and its corresponding confounds TSV (fmriprep format) are adjusted to remove the first n seconds of data.

Mandatory Inputs:

  • bold_file (a pathlike object or string representing an existing file) – Either cifti or nifti .

  • confounds_file (a pathlike object or string representing an existing file) – TSV file with selected confounds for denoising.

  • dummy_scans (an integer or ‘auto’) – Number of volumes to drop from the beginning, calculated in an earlier workflow from dummy_scans.

  • fmriprep_confounds_file (a pathlike object or string representing an existing file) – FMRIPrep confounds tsv. Used for motion-based censoring.

  • motion_file (a pathlike object or string representing an existing file) – Confounds file containing only filtered motion parameters.

  • temporal_mask (a pathlike object or string representing an existing file) – Temporal mask file.

Outputs:

  • bold_file_dropped_TR (a pathlike object or string representing an existing file) – Bold or cifti with volumes dropped.

  • confounds_file_dropped_TR (a pathlike object or string representing an existing file) – TSV file with selected confounds for denoising, after removing TRs.

  • dummy_scans (an integer) – Number of volumes dropped.

  • fmriprep_confounds_file_dropped_TR (a pathlike object or string representing an existing file) – FMRIPrep confounds tsv after removing TRs. Used for motion-based censoring.

  • motion_file_dropped_TR (a pathlike object or string representing an existing file) – Confounds file containing only filtered motion parameters.

  • temporal_mask_dropped_TR (a pathlike object or string representing an existing file) – Temporal mask file.