Preprocessing fMRI Data
OverviewTeaching: 30 min
Exercises: 0 minQuestions
What are the standard preprocessing steps?
What existing pipelines help with preprocessing?Objectives
Understand the common preprocessing steps
Slice Timing Correction
Susceptibility Distortion Correction
Artifact and Structured Noise Removal
Volume Censoring (Scrubbing)
fmriprep is a package developed by the Poldrack lab to do the minimal preprocessing of fMRI data required. It covers brain extraction, motion correction, field unwarping, and registration. It uses a combination of well-known software packages (e.g., FSL, SPM, ANTS, AFNI) and selects the ‘best’ implementation of each preprocessing step.
fmriprep can be invoked from the command line. We can even run it inside this notebook! The following command should work after you remove the ‘hashtag’
However, running fmriprep takes quite some time (we included the hashtag to prevent you from accidentally running it). You’ll most likely want to run it in parallel on a computing cluster.
fmriprep takes care of several of the preprocessing steps