fmriprep - Preprocess task-based and resting-state fMRI
Preprocess BIDS-organized task-based or resting-state fMRI data with fMRIPrep and produce BIDS-Derivatives and subject-level HTML reports.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Preprocess BIDS fMRI data
- Configure container execution
- Select output spaces
- Configure distortion correction
- Extract confounds tables
- Resample surface data
- Interpret visual reports
- Debug pipeline failures
- Reuse derivatives
- Generate citation boilerplate
Inputs
- BIDS dataset
- Output directory
- Working directory
- Participant labels
- Output-space specifications
- Fieldmap metadata
- FreeSurfer license file
- TemplateFlow templates
- Container runtime
- BIDS filter file
- Derivative datasets
Outputs
- BIDS-Derivatives dataset
- Subject-level HTML report
- Confounds TSV files
- Surface-resampled data
- CIFTI outputs
- Pipeline logs
- Citation boilerplate
Requirements
- Python 3.10 or later
- Docker, Apptainer, or Singularity
- FreeSurfer license
- Compatible fMRIPrep environment
- TemplateFlow access or cached templates
- Internet access for uncached resources