Warning: This document is for an old version of smriprep. The main version is master.

sMRIPrep: Structural MRI PREProcessing pipeline

sMRIPrep is a structural magnetic resonance imaging (sMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (subject-wise averaging, B1 field correction, spatial normalization, segmentation, skullstripping etc.) providing outputs that can be easily connected to subsequent tools such as fMRIPrep or dMRIPrep.

The workflow is based on Nipype and encompases a combination of tools from well-known software packages, including FSL, ANTs, FreeSurfer, and AFNI.

More information and documentation can be found at https://www.nipreps.org/smriprep/. Support is provided on neurostars.org.

Principles

sMRIPrep is built around three principles:

1. Robustness - The pipeline adapts the preprocessing steps depending on the input dataset and should provide results as good as possible independently of scanner make, scanning parameters or presence of additional correction scans (such as fieldmaps).

2. Ease of use - Thanks to dependence on the BIDS standard, manual parameter input is reduced to a minimum, allowing the pipeline to run in an automatic fashion.

3. “Glass box” philosophy - Automation should not mean that one should not visually inspect the results or understand the methods. Thus, sMRIPrep provides visual reports for each subject, detailing the accuracy of the most important processing steps. This, combined with the documentation, can help researchers to understand the process and decide which subjects should be kept for the group level analysis.

Acknowledgements

Please acknowledge this work by mentioning explicitly the name of this software (sMRIPrep) and the version, along with a link to the GitHub repository or the Zenodo reference (doi:10.5281/zenodo.2650521).

Contents

• Installation
  • Container technologies: Docker and Singularity
    • Docker (recommended for PC/laptop and commercial Cloud)
    • Singularity (recommended for HPC)
  • Manually Prepared Environment (Python 3.5+)
    • External Dependencies
• Usage
  • Execution and the BIDS format
  • Command-Line Arguments
    • Positional Arguments
    • Named Arguments
    • Options for filtering BIDS queries
    • Options to handle performance
    • Workflow configuration
    • Specific options for ANTs registrations
    • Specific options for FreeSurfer preprocessing
    • Surface preprocessing options
    • Other options
  • The command-line interface of the docker wrapper
    • Positional Arguments
    • Named Arguments
    • Wrapper options
    • Developer options
  • The FreeSurfer license
• Library API (application program interface)
  • smriprep.cli package
    • Submodules
  • smriprep.interfaces package
    • DerivativesDataSink
    • Submodules
  • smriprep.utils package
    • Submodules
  • smriprep.workflows package
    • Submodules
• What’s new?
  • 0.8.0 (TBD)
  • 0.7.1 (November 18, 2020)
  • 0.7.0 (September 27, 2020)
  • 0.6.2 (June 9, 2020)
  • 0.6.1 (May 27, 2020)
  • 0.6.0 (May 22, 2020)
  • 0.5.x Series
    • 0.5.3 (June 7, 2020)
    • 0.5.2 (February 14, 2020)
    • 0.5.1 (February 7, 2020)
    • 0.5.0 (February 6, 2020)
  • Pre- 0.5.x Series
    • 0.4.2 (January 22, 2020)
    • 0.4.1 (Decemeber 12, 2019)
    • 0.4.0 (November 26, 2019)
    • 0.3.2 (September 9, 2019)
    • 0.3.1 (July 21, 2019)
    • 0.3.0 (July 12, 2019)
    • 0.2.4 (July 9, 2019)
    • 0.2.3 (June 5, 2019)
    • 0.2.2 (June 5, 2019)
    • 0.2.1 (May 6, 2019)
    • 0.2.0 (May 3, 2019)
    • 0.1.1 (March 22, 2019)
    • 0.1.0 (March 05, 2019)
    • 0.0.5 (February 06, 2019)
    • 0.0.4 (January 25, 2019)
    • 0.0.3 (January 18, 2019)
    • 0.0.2 (January 8, 2019)