Developers - API

xcp_d-combineqc

Aggregate qc of all the subjects.

usage: xcp_d-combineqc [-h] [--cifti] xcpd_dir output_prefix

Positional Arguments

xcpd_dir

xcp_d output dir

output_prefix

output prefix for group

Named Arguments

--cifti

add cifti qc files

Default: False

xcp_d.workflow: Workflows

Nipype workflows for xcp_d.

workflow.base	The primary workflows for xcp_d.
workflow.bold	Workflows for post-processing the BOLD data.
workflow.cifti	Workflows for post-processing CIFTI-format BOLD data.
workflow.anatomical	Anatomical post-processing workflows.
workflow.connectivity	Workflows for extracting time series and computing functional connectivity.
workflow.execsummary	Workflows for generating the executive summary.
workflow.outputs	Workflows for collecting and saving xcp_d outputs.
workflow.plotting	Plotting workflows.
workflow.postprocessing	Workflows for post-processing BOLD data.
workflow.restingstate	Workflows for calculating resting state-specific metrics.

xcp_d.interfaces: Nipype Interfaces

Initialize interfaces.

interfaces.ants	ANTS interfaces.
interfaces.bids	Nipype interfaces for working with BIDS data.
interfaces.c3	Convert3D is a command-line tool for converting 3D images between common file formats.
interfaces.connectivity	Handling functional connectvity.
interfaces.filtering	Handling filtering.
interfaces.layout_builder	Classes for building an executive summary file.
interfaces.nilearn	Interfaces for Nilearn code.
interfaces.prepostcleaning	Interfaces for the post-processing workflows.
interfaces.qc_plot	Quality control plotting interfaces.
interfaces.regression	Regression interfaces.
interfaces.report_core	Tools for generating Reports.
interfaces.report	Interfaces to generate reportlets.
interfaces.resting_state	Interfaces for working with resting-state fMRI data.
interfaces.surfplotting	Surface plotting interfaces.
interfaces.workbench	Custom wb_command interfaces.

xcp_d.utils: Miscellaneous Utility Functions

A range of utility functions for xcp_d interfaces and workflows.

utils.atlas	Functions for working with atlases.
utils.bids	Utilities for fmriprep bids derivatives and layout.
utils.concatenation	Functions for concatenating scans across runs.
utils.confounds	Confound matrix selection based on Ciric et al. 2007.
utils.dcan2fmriprep	Functions for converting DCAN-format derivatives to fMRIPrep format.
utils.hcp2fmriprep	Functions for converting HCP-format data to fMRIPrep format.
utils.doc	Functions related to the documentation.
utils.execsummary	Functions for generating the executive summary.
utils.fcon	Functions for calculating functional connectivity in NIFTI files.
utils.filemanip	Miscellaneous file manipulation functions.
utils.modified_data	Functions for interpolating over high-motion volumes.
utils.plot	Plotting tools.
utils.qcmetrics	Quality control metrics.
utils.sentry	Stripped out routines for Sentry.
utils.utils	Miscellaneous utility functions for xcp_d.
utils.write_save	Utilities to read and write nifiti and cifti data.