A scalable method to improve gray matter segmentation at ultra high field MRI

PLoS One. 2018 Jun 6;13(6):e0198335. doi: 10.1371/journal.pone.0198335. eCollection 2018.

Abstract

High-resolution (functional) magnetic resonance imaging (MRI) at ultra high magnetic fields (7 Tesla and above) enables researchers to study how anatomical and functional properties change within the cortical ribbon, along surfaces and across cortical depths. These studies require an accurate delineation of the gray matter ribbon, which often suffers from inclusion of blood vessels, dura mater and other non-brain tissue. Residual segmentation errors are commonly corrected by browsing the data slice-by-slice and manually changing labels. This task becomes increasingly laborious and prone to error at higher resolutions since both work and error scale with the number of voxels. Here we show that many mislabeled, non-brain voxels can be corrected more efficiently and semi-automatically by representing three-dimensional anatomical images using two-dimensional histograms. We propose both a uni-modal (based on first spatial derivative) and multi-modal (based on compositional data analysis) approach to this representation and quantify the benefits in 7 Tesla MRI data of nine volunteers. We present an openly accessible Python implementation of these approaches and demonstrate that editing cortical segmentations using two-dimensional histogram representations as an additional post-processing step aids existing algorithms and yields improved gray matter borders. By making our data and corresponding expert (ground truth) segmentations openly available, we facilitate future efforts to develop and test segmentation algorithms on this challenging type of data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Female
  • Gray Matter / anatomy & histology*
  • Gray Matter / diagnostic imaging
  • Humans
  • Image Processing, Computer-Assisted
  • Magnetic Fields
  • Magnetic Resonance Imaging / methods*
  • Male

Grants and funding

This work was financed by the Netherlands Organisation for Scientific Research (NWO; https://www.nwo.nl/en). The authors O.F.G. and F.D.M. as well as data acquisition for the MPRAGE data set were supported by NWO VIDI grant 864-13-012. Author M.S. was supported by NWO research talent grant 406-14-108. Author I.M. was supported by NWO research talent grant 406-14-085. Author R.H. and acquisition of the MP2RAGE was funded by Technology Foundation STW (http://www.stw.nl/en/) grant 12724.