dcan-labs / dcan-hcp

The DCAN Lab's version of the minimal preprocessing pipeline for the Human Connectome Project

DCAN-HCP Pipelines

This repository is the DCAN labs' modified HCP Pipelines for the processing of functional MRI images.

The original HCP Pipelines is a set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project, as outlined in Glasser et al. 2013. The original pipeline software is available here

In particular, the DCAN labs repository includes several modifications of primary shell scripts for processing functional MRI data.

The changes include:

• updating the nonlinear registration tool to ANTs
• using denoising and N4BiasCorrection to increase consistency over extreme noise or bias in anatomical scans
• optional processing with no T2-weighted image
• adjusting the order of some image processing operations
• several additional options for processing

This is the backend component for the processing of data. It is not designed for direct use as a user interface. For the pipeline interface in the form of a dockerized bids application, please refer to the official application repository.

dcan-hcp's Issues

Clarification of ACPC template

In PreFreeSurferPipeline.sh, it mentions that 0.7mm MNI template is used for ACPC alignment. However, in ACPCAlignment.sh, 1mm template is used as default. It would be better to clarify which template will be used and correct the log message and comments in PreFreeSurferPipeline.