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Ironsmith: An automated pipeline for QSM-based data analyses.

Valentinos Zachariou1, Christopher E Bauer1, David K Powell2

  • 1Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY 40536-0298 United States.

Neuroimage
|December 22, 2021
PubMed
Summary

Ironsmith is a new, open-source pipeline for automated quantitative susceptibility mapping (QSM) analysis of brain iron. It reliably extracts QSM values from 89 ROIs, aiding research into neurodegenerative diseases and aging.

Keywords:
AgingAutomated pipelineBrain ironQuantitative susceptibility mappingSoftware

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Area of Science:

  • Neuroimaging
  • Biomarker Quantification
  • Computational Neuroscience

Background:

  • Quantitative susceptibility mapping (QSM) is an MRI technique for measuring iron concentration in brain tissue.
  • Existing QSM software lacks automated analysis pipelines and quality control measures.
  • Brain iron is implicated in neurological disorders and cognitive aging.

Purpose of the Study:

  • To introduce Ironsmith, an open-source, automated pipeline for QSM data analysis.
  • To demonstrate the reliability and external validity of the Ironsmith pipeline.
  • To provide a tool for researchers studying brain iron in aging and neurodegeneration.

Main Methods:

  • Developed Ironsmith, a fully automated pipeline from DICOM to ROI-based QSM values.
  • Incorporated quality control measures including SNR and outlier assessment.
  • Utilized CSF-only masks to minimize partial volume effects.
  • Extracted QSM values from 89 subcortical and cortical brain regions.

Main Results:

  • Ironsmith demonstrated excellent intra- and inter-rater reliability.
  • External validity was confirmed by an association between motor performance and motor cortex QSM values.
  • Automated filtering of QSM outlier values was successfully implemented.

Conclusions:

  • Ironsmith offers a reliable, turn-key solution for automated QSM analysis.
  • The pipeline supports research on the role of brain iron in aging and neurodegenerative diseases.
  • This tool addresses the need for standardized and validated QSM data processing.