Impact of acquisition protocols and processing streams on tissue segmentation of T1 weighted MR images

Kristi A. Clark, Roger P. Woods, David A. Rottenberg, Arthur W. Toga, John C. Mazziotta

Research output: Contribution to journalArticlepeer-review

47 Scopus citations


The segmentation of T1-weighted images into gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) is a fundamental processing step in neuroimaging, the results of which affect many other structural imaging analyses. Variability in the segmentation process can decrease the power of a study to detect anatomical differences, and minimizing such variability can lead to more robust results. This paper outlines a straightforward strategy that can be used (1) to select more optimal data acquisition and processing protocols and (2) to quantify the impact of such optimization. Using this approach with multiple scans of a single subject, we found that the choice of a segmentation algorithm had the largest impact on variability, while the choice of a pulse sequence had the second largest impact. The data indicate that the classification of GM is the most variable, and that the optimal protocol may differ across tissue types. Therefore, the intended use of segmentation data should play a role in optimization. Examples are provided to demonstrate that the minimization of variability is not sufficient for optimization; the overall accuracy of the approach must also be considered. Simple volumetric computations are included to illustrate the potential gain of optimization; these results show that volume estimates from optimal pathways were on average three times less variable than estimates from suboptimal pathways. Therefore, the simple strategy illustrated here can be applied to many studies to optimize tissue segmentation, which should lead to a net increase in the power of structural neuroimaging studies.

Original languageEnglish (US)
Pages (from-to)185-202
Number of pages18
Issue number1
StatePublished - Jan 1 2006


  • MRI
  • Reliability
  • Segmentation
  • Structural neuroimaging
  • Tissue classification
  • Validation

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