This lesson is still being designed and assembled (Pre-Alpha version)

sMRI Analysis: Reproducibility Considerations

Overview

Teaching: 20 min
Exercises: 10 min
Questions
  • How sensitive are the findings to your MR pipeline parameters?

Objectives
  • Understand impact of software and atlas choices

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MR image processing pipeline selection choices

Example software analysis

Task: compare cortical thickness between FreeSurfer and CIVET

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Note: See this 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.