._dep_05-preprocessing.md

title	teaching	exercises	questions	objectives	keypoints
Preprocessing fMRI Data	0	0	What are the standard preprocessing steps? What existing pipelines help with preprocessing?	Understand the common preprocessing steps	fmriprep takes care of several of the preprocessing steps

Preprocessing Steps

T1w Preprocessing

Despiking

Motion Correction

Slice Timing Correction

Susceptibility Distortion Correction

Artifact and Structured Noise Removal

Volume Censoring (Scrubbing)

Bandpass Filtering

Spatial Smoothing

Normalization

Using fmriprep

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. Once installed, 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.

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