Sub-millimeter isotropic MRI for segmentation of subcortical brain regions and brain visualization

Ying Wu*, Ann B. Ragin, Hongyan Du, Shawn Sidharthan, Eugene E. Dunkle, Ioannis Koktzoglou, Robert R. Edelman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Purpose: To evaluate a rapid sub-millimeter isotropic spoiled gradient-echo (nonselective SPGR) to facilitate the brain subcortical segmentation and the visualization of brain volume compared with the commonly accepted inversion recovery-prepared SPGR (SPGR-IR) technique. Materials and Methods: The feasibility of the nonselective SPGR was evaluated for two segmentation algorithms. FAST was used to segment the brain into constituent tissue classes (white matter, gray matter, cerebrospinal fluid) and FreeSurfer was used to segment specific subcortical structures (hippocampus, caudate, putamen, and thalamus). Localized apparent signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) values for nonselective SPGR and the SPGR-IR were compared for the studied subcortical regions. The three-dimensional volume rendering was generated to evaluate the nonselective SPGR and the SPGR-IR for brain visualization. Results: In basal ganglia regions, nonselective SPGR allows for consistent segmentation results for both FAST and Free-Surfer. This sequence also better differentiated gray/white matter compared with SPGR-IR. An approximate two-fold improvement of image quality in apparent SNR and CNR was indicated for subcortical brain anatomical structures with nonselective SPGR versus SPGR-IR. The nonselective SPGR improved clarity and yielded a more realistic depiction of the brain surface for visualization compared with SPGR-IR. Conclusion: Compared with SPGR-IR, nonselective SPGR allows for consistent segmentation results for basal ganglia regions and improved clarity for visualization of the brain.

Original languageEnglish (US)
Pages (from-to)980-986
Number of pages7
JournalJournal of Magnetic Resonance Imaging
Issue number4
StatePublished - Apr 2010


  • High resolution MRI
  • Isotropic MRI
  • Segmentation
  • Subcortical brain
  • Visualization

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging


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