Setting Up A Pipeline Configuration

Overview

This section explains how to create a new pipeline or edit an existing one. If you wish to use one of the pre-configured pipelines that come packaged with C-PAC, you can view the current available library of pipelines here.

Neuroparc v1.0: Baseline

On July 20, 2020, Neuroparc released v1.0. In moving from v0 to v1, the paths to several of the Neuroparc atlases changed. The atlases are used by C-PAC in its default and preconfigured pipelines. C-PAC v1.7.0 includes the Neuroparc v1.0 paths, but if you are using a pipeline based on C-PAC 1.6.2a or older, you will need to update any Nueroparc v0 paths in your config

All paths begin with /ndmg_atlases/label/Human/

Neuroparc v0	Neuroparc v1
aal_space-MNI152NLin6_res-1x1x1.nii.gz	AAL_space-MNI152NLin6_res-1x1x1.nii.gz
aal_space-MNI152NLin6_res-2x2x2.nii.gz	AAL_space-MNI152NLin6_res-2x2x2.nii.gz
AAL2zourioMazoyer2002.nii.gz	AAL_space-MNI152NLin6_res-1x1x1.nii.gz
brodmann_space-MNI152NLin6_res-1x1x1.nii.gz	Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz
brodmann_space-MNI152NLin6_res-2x2x2.nii.gz	Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz
CorticalAreaParcellationfromRestingStateCorrelationsGordon2014.nii.gz	CAPRSC_space-MNI152NLin6_res-1x1x1.nii.gz
desikan_space-MNI152NLin6_res-1x1x1.nii.gz	Desikan_space-MNI152NLin6_res-1x1x1.nii.gz
desikan_space-MNI152NLin6_res-2x2x2.nii.gz	Desikan_space-MNI152NLin6_res-2x2x2.nii.gz
DesikanKlein2012.nii.gz	DesikanKlein_space-MNI152NLin6_res-1x1x1.nii.gz
glasser_space-MNI152NLin6_res-1x1x1.nii.gz	Glasser_space-MNI152NLin6_res-1x1x1.nii.gz
Juelichgmthr252mmEickhoff2005.nii.gz	Juelich_space-MNI152NLin6_res-1x1x1.nii.gz
MICCAI2012MultiAtlasLabelingWorkshopandChallengeNeuromorphometrics.nii.gz	MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz
princetonvisual-top_space-MNI152NLin6_res-2x2x2.nii.gz	Princetonvisual-top_space-MNI152NLin6_res-2x2x2.nii.gz
Schaefer2018-200-node_space-MNI152NLin6_res-1x1x1.nii.gz	Schaefer200_space-MNI152NLin6_res-1x1x1.nii.gz
Schaefer2018-300-node_space-MNI152NLin6_res-1x1x1.nii.gz	Schaefer300_space-MNI152NLin6_res-1x1x1.nii.gz
Schaefer2018-400-node_space-MNI152NLin6_res-1x1x1.nii.gz	Schaefer400_space-MNI152NLin6_res-1x1x1.nii.gz
Schaefer2018-1000-node_space-MNI152NLin6_res-1x1x1.nii.gz	Schaefer1000_space-MNI152NLin6_res-1x1x1.nii.gz
slab907_space-MNI152NLin6_res-1x1x1.nii.gz	Slab907_space-MNI152NLin6_res-1x1x1.nii.gz
yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz	Yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz
yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz	Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz
yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz	Yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz
yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz	Yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz

There are two ways of setting up or editing a pipeline configuration for C-PAC:

• Using the pipeline configuration interface in the C-PAC GUI

• Using a text editor (useful for remote servers where using the C-PAC GUI is not possible or impractical)

Definitions

• Workflow

  A workflow accomplishes a particular processing task (e.g. functional preprocessing, scrubbing, nuisance correction). Each workflow can be turned on or off in the pipeline configuration. Sometimes a workflow can be set to both on and off, allowing for pipelines to branch.

• Pipeline

  A pipeline is a combination of workflows.

• Strategy

  A strategy is a set of preprocessing options. Specifically, a strategy is defined by nuisance corrections and scrubbing settings. Strategies can branch depending on which of these workflows are turned on or off and how they are configured.

• Derivative

  Derivatives are the results of processing a participant’s raw data (i.e., connectivity measures).

• Atlas

  An atlas provides a guide to the location of anatomical features in a coordinate space.

  —[1] p. 55

  An atlas provides a defined coordinate space, a template for aligning images, and labels for regions of interest.

  Currently C-PAC only supports atlases in NifTI format.

  CIFTI is a popular atlas format not yet supported by C-PAC. As always, if anyone wants to share any tips or hacks with us, we are an open-source platform after all. Below are some resources that might help enable CIFTI atlas support in a future version of C-PAC.

  CIFTI Resources

  • Mejia, M. 2015 August. A layman’s guide to working with CIFTI files, Mandy Mejia.

  • Habeeb, H. 2018 December. Convert from CIFTI2 (HCP) to 3D array, Neurostars.

  • Etzel, J. 2014 March. NIfTI, CIFTI, GIFTI in the HCP and Workbench: a primer, MVPA meanderings.

• Template

  A template is an image that is representative of the atlas and provides a target to which individual images can be aligned.

  —[1] p. 55

  C-PAC images include the following templates:

  path in container	source
  /ants_template/oasis	ANTs/ANTsR Brain Templates: OASIS.zip
  /cpac_templates	C-PAC Templates
  /ndmg_atlases	Neuroparc v1.0: Baseline
  /opt/dcan-tools/pipeline/global/templates	DCAN-HCP Pipelines: global/templates
  /usr/share/data/fsl-mni152-templates	fsl-mni152-templates – MNI152 stereotaxic brain templates for FSL
  /usr/share/fsl/5.0/data/atlases	fsl-atlases – FSL’s MNI152 standard space stereotaxic brain atlases http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz
  /usr/share/fsl/5.0/data/standard	http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz

Reference

[1] (1,2)

Poldrack, R. A., Mumford, J. A., and Nichols, T. E. 2011 August. Handbook of Functional MRI Data Analysis. New York: Cambridge University Press.