fMRIproc Documentation

Welcome to the fMRIproc documentation. This pipeline is designed for the acquisition and post-processing of line scanning and whole-brain/partial FOV BOLD data at the Spinoza Centre for Neuroimaging. This repository contains all of the tools used during the acquisition and postprocessing of line scanning data at the Spinoza Centre for Neuroimaging in Amsterdam. Over time, it has evolved to also incorporate regular whole-brain/partial FOV BOLD data. The main goal of the package is to create the most accurate segmentations (both volumetric and surface) by combining various software packages such as Nighres, fMRIprep, FreeSurfer, and CAT12. This package contains the minimum for the preprocessing of anatomical and functional data as well as denoising with Pybest and population receptive field routines with pRFpy. HRF estimation, plotting, and other analysis approaches performed in my line-scanning projects can be found in the lazyfmri-repository.

Contents

• Installation Guide
  • Setting Up the Environment
  • Configuring the Environment
• Overview of fMRIproc
  • Main Features
  • Why Use fMRIproc?
• Configuration Setup
  • Example spinoza_config
  • Running fMRIproc on clusters
  • Setting up fmriprep-docker
  • Setting up Matlab Runtime
  • Setting up Nighres
• Pipeline Steps
  • Step-by-step run-through
  • Vanilla pipeline
  • Tips for FSL’s FEAT
• Required External Software
• Running fMRIproc on HPC Clusters
  • Check Scheduler Type
  • Submitting Jobs
• Troubleshooting & Common Issues
  • Issue: fMRIprep Cannot Find License File
  • Issue: Error with Cluster Submission
  • Issue: Incorrect Phase-Encoding Direction

Example gallery

• Using the lazyfmri-package
• Using the pRFmodelFitter-class
• View pRF results on surface

Reference

• Python modules
• Bash modules