Developers - API

xcp_d-combineqc

Aggregate qc of all the subjects.

usage: xcp_d-combineqc [-h] xcpd_dir output_prefix

Positional Arguments

xcpd_dir

xcp_d output dir

output_prefix

output prefix for group

xcp_d.workflows: Workflows

Nipype workflows for xcp_d.

xcp_d.workflows.base

The primary workflows for xcp_d.

xcp_d.workflows.bold

Workflows for post-processing the BOLD data.

xcp_d.workflows.cifti

Workflows for post-processing CIFTI-format BOLD data.

xcp_d.workflows.anatomical

Anatomical post-processing workflows.

xcp_d.workflows.concatenation

Workflows for concatenating postprocessed data.

xcp_d.workflows.connectivity

Workflows for extracting time series and computing functional connectivity.

xcp_d.workflows.execsummary

Workflows for generating the executive summary.

xcp_d.workflows.outputs

Workflows for collecting and saving xcp_d outputs.

xcp_d.workflows.plotting

Plotting workflows.

xcp_d.workflows.postprocessing

Workflows for post-processing BOLD data.

xcp_d.workflows.restingstate

Workflows for calculating resting state-specific metrics.

xcp_d.interfaces: Nipype Interfaces

Initialize interfaces.

xcp_d.interfaces.ants

ANTS interfaces.

xcp_d.interfaces.bids

Adapted interfaces from Niworkflows.

xcp_d.interfaces.c3

Convert3D is a command-line tool for converting 3D images between common file formats.

xcp_d.interfaces.concatenation

Interfaces for the concatenation workflow.

xcp_d.interfaces.connectivity

Handling functional connectvity.

xcp_d.interfaces.execsummary

Classes for building an executive summary file.

xcp_d.interfaces.nilearn

Interfaces for Nilearn code.

xcp_d.interfaces.plotting

Plotting interfaces.

xcp_d.interfaces.censoring

Interfaces for the post-processing workflows.

xcp_d.interfaces.report_core

Tools for generating Reports.

xcp_d.interfaces.report

Interfaces to generate reportlets.

xcp_d.interfaces.restingstate

Interfaces for working with resting-state fMRI data.

xcp_d.interfaces.utils

Miscellaneous utility interfaces.

xcp_d.interfaces.workbench

Custom wb_command interfaces.

xcp_d.utils: Miscellaneous Utility Functions

A range of utility functions for xcp_d interfaces and workflows.

xcp_d.utils.atlas

Functions for working with atlases.

xcp_d.utils.bids

Utilities for fmriprep bids derivatives and layout.

xcp_d.utils.concatenation

Functions for concatenating scans across runs.

xcp_d.utils.confounds

Confound matrix selection based on Ciric et al. 2007.

xcp_d.utils.doc

Functions related to the documentation.

xcp_d.utils.execsummary

Functions for generating the executive summary.

xcp_d.utils.filemanip

Miscellaneous file manipulation functions.

xcp_d.utils.modified_data

Functions for interpolating over high-motion volumes.

xcp_d.utils.plotting

Plotting tools.

xcp_d.utils.qcmetrics

Quality control metrics.

xcp_d.utils.restingstate

Functions for calculating resting-state derivatives (ReHo and ALFF).

xcp_d.utils.sentry

Stripped out routines for Sentry.

xcp_d.utils.utils

Miscellaneous utility functions for xcp_d.

xcp_d.utils.write_save

Utilities to read and write nifiti and cifti data.

xcp_d.ingression: Functions to Ingress Preprocessing Derivatives

Tools for converting derivatives from various pipelines to an fMRIPrep-like format.

xcp_d.ingression.abcdbids

Functions for converting ABCD-BIDS-format derivatives to fMRIPrep format.

xcp_d.ingression.hcpya

Functions for converting HCP-YA-format data to fMRIPrep format.

xcp_d.ingression.ukbiobank

Functions to convert preprocessed UK Biobank BOLD data to BIDS derivatives format.

xcp_d.ingression.utils

Functions to support ingression of non-BIDS preprocessing derivatives.