sMRI Analysis: Reproducibility Considerations

Last updated on 2025-02-26 | Edit this page

Estimated time: 30 minutes

Overview

Questions

  • How sensitive are the findings to your MR pipeline parameters?

Objectives

  • Understand impact of software and atlas choices

You Are Here!

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MR image processing pipeline selection choices

  • Compute environment

    • OS / system math libraries
    • Programming libraries Python / R versions

  • Software (algorithms and their versions)

    • Image clean-up
    • Image normalization
    • Image quantification

  • Quality control

    • Manual protocol specifics
    • Automatic outlier criteria

  • Biological priors

    • Templates
    • Atlases/parcellations: ROI definitions

Example software analysis

Task: compare cortical thickness between FreeSurfer and CIVET

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Note: See this article for details on brain plots

Correlation between thickness measurements:

Software: FreeSurfer (v5.1, v5.3, v6.0), CIVET (2.1) and ANTs

Parcellation: DKT

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Possible choices for FreeSurfer parcellations

Different parcellation different results?

Inference pertaining to neuroantomical differences and/or prediction models based on individual neuroanatomical feature sets can be sensitive to parcellation choice.

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Note: Image adopted from Madan 2021

Key Points
  • It is crucial to assess biological vs methodological variation in your findings to avoid reproducibility crisis.