Individual skill

fmriprep

Preprocess task-based or resting-state fMRI data with fMRIPrep — a robust, BIDS-App preprocessing pipeline built on FSL, ANTs, FreeSurfer, AFNI, and Nilearn. Use this skill whenever the user asks to preprocess fMRI/BOLD data, run fMRIPrep on a BIDS dataset, set up Docker/Singularity/Apptainer containers for fMRIPrep, choose output spaces (MNI152NLin2009cAsym, fsaverage, fsLR/CIFTI), configure susceptibility distortion correction (SDC), extract or interpret the confounds table, resample to surface/grayordinates, cite fMRIPrep and its dependencies, or debug fMRIPrep crashes and hangs.

packages/skills/skills/06_fMRI_Neuroimaging/fmriprep/SKILL.md

Source commit 93f685577b683843f2b1d851cd6dc5f7f1d89221

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Observed behavior

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Last checked

Nov 3, 2026

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