A critical assessment of data quality and venous effects in sub-millimeter fMRI

Kendrick N Kay, Keith W. Jamison, Luca Vizioli, Ruyuan Zhang, Eshed Margalit, Kamil Ugurbil

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Advances in hardware, pulse sequences, and reconstruction techniques have made it possible to perform functional magnetic resonance imaging (fMRI) at sub-millimeter resolution while maintaining high spatial coverage and acceptable signal-to-noise ratio. Here, we examine whether sub-millimeter fMRI can be used as a routine method for obtaining accurate measurements of fine-scale local neural activity. We conducted fMRI in human visual cortex during a simple event-related visual experiment (7 T, gradient-echo EPI, 0.8-mm isotropic voxels, 2.2-s sampling rate, 84 slices), and developed analysis and visualization tools to assess the quality of the data. Our results fall along three lines of inquiry. First, we find that the acquired fMRI images, combined with appropriate surface-based processing, provide reliable and accurate measurements of fine-scale blood oxygenation level dependent (BOLD) activity patterns. Second, we show that the highly folded structure of cortex causes substantial biases on spatial resolution and data visualization. Third, we examine the well-recognized issue of venous contributions to fMRI signals. In a systematic assessment of large sections of cortex measured at a fine scale, we show that time-averaged T 2 *-weighted EPI intensity is a simple, robust marker of venous effects. These venous effects are unevenly distributed across cortex, are more pronounced in gyri and outer cortical depths, and are, to a certain degree, in consistent locations across subjects relative to cortical folding. Furthermore, we show that these venous effects are strongly correlated with BOLD responses evoked by the experiment. We conclude that sub-millimeter fMRI can provide robust information about fine-scale BOLD activity patterns, but special care must be exercised in visualizing and interpreting these patterns, especially with regards to the confounding influence of the brain's vasculature. To help translate these methodological findings to neuroscience research, we provide practical suggestions for both high-resolution and standard-resolution fMRI studies.

Original languageEnglish (US)
Pages (from-to)847-869
Number of pages23
StatePublished - Apr 1 2019

Bibliographical note

Funding Information:
We thank E. Yacoub for assistance with pulse sequences and B. Adeyemo, P. Bandettini, K. Grill-Spector, L. Huber, S. Moeller, S. Petersen, K. Weiner, and J. Winawer for helpful discussions. We also thank J. Carlin, I. Marquardt, and R. Turner for comments on the manuscript. This work was supported by NIH Grants P41 EB015894 , P30 NS076408 , S10 RR026783 , S10 OD017974-01 , U01 EB025144 , and the W. M. Keck Foundation.


  • BOLD signal
  • Cortical curvature
  • Cortical depth
  • High-resolution fMRI
  • Vasculature
  • Veins

Fingerprint Dive into the research topics of 'A critical assessment of data quality and venous effects in sub-millimeter fMRI'. Together they form a unique fingerprint.

Cite this