Welcome to clpipe: A MRI Processing Pipeline for high performance clusters!

clpipe was developed to streamline the processing of MRI data using the high performance cluster at University of North Carolina at Chapel Hill. It uses fmriprep for preprocessing fMRI data and implements a variety of additional processing steps important for functional connectivity analyses such as nuisance regression and filtering. Also included in clpipe are a variety of console commands for validation and checking the results of preprocessing. Please report any bugs, issues or feature requests on our Github page.

Documentation

• Installation
• Overview
• Project Setup
• DICOM to BIDs Conversion
• BIDS Validation
• Preprocessing with fMRIprep
• Postprocessing
• GLM Analysis
• ROI Extraction
• Flywheel Sync
• Change Log

Tutorial

• Project Setup
• BIDS Conversion
• BIDS Validation