fMRIPrep: Robust fMRI Preprocessing Pipeline¶
Library: fMRIPrep | Docker Image: nipreps/fmriprep
Function¶
Automated, robust preprocessing pipeline for task-based and resting-state fMRI, combining tools from FSL, FreeSurfer, ANTs, and AFNI with best practices.
Modality: BIDS-formatted dataset containing T1w anatomical and BOLD fMRI data (NIfTI format).
Typical Use: Complete standardized fMRI preprocessing from BIDS data to analysis-ready outputs.
Key Parameters¶
Key Points¶
Requires BIDS-formatted input. Handles brain extraction, segmentation, registration, motion correction, distortion correction, and confound estimation. Generates comprehensive visual QC reports.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
bids_dir |
Directory |
Yes | BIDS dataset directory | |
output_dir |
string |
Yes | Output directory | |
analysis_level |
string |
Yes | Analysis level (participant) | |
participant_label |
string |
No | Participant label (without sub- prefix) | --participant-label |
output_spaces |
string |
No | Output spaces (e.g., MNI152NLin2009cAsym) | --output-spaces |
fs_license_file |
File |
No | FreeSurfer license file | --fs-license-file |
nprocs |
int |
No | Number of processors | --nprocs |
mem_mb |
int |
No | Memory limit (MB) | --mem-mb |
skip_bids_validation |
boolean |
No | Skip BIDS validation | --skip-bids-validation |
Accepted Input Extensions¶
- fs_license_file:
.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
log |
File |
fmriprep.log |
Docker Tags¶
Available versions: latest, unstable, 25.2.4, premask, 25.2.3, 25.2.2, 25.2.1, 25.2.0, pre-release, 25.1.4
and 5 more
Categories¶
- Functional MRI > fMRIPrep > Pipeline
- Pipelines > fMRIPrep > fMRI Preprocessing