Optimization of functional MRI for detection, decoding and high-resolution imaging of the response patterns of cortical columns

Denis Chaimow, Kâmil Uğurbil, Amir Shmuel

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


The capacity of functional MRI (fMRI) to resolve cortical columns depends on several factors. These include the spatial scale of the columnar pattern, the point-spread of the fMRI response, the voxel size, and the signal-to-noise ratio (SNR) considering thermal and physiological noise. However, it remains unknown how these factors combine, and what is the voxel size that optimizes fMRI of cortical columns. Here we combine current knowledge into a quantitative model of fMRI of realistic patterns of cortical columns with different spatial scales and degrees of irregularity. We compare different approaches for identifying patterns of cortical columns, including univariate and multivariate based detection, multi-voxel pattern analysis (MVPA) based decoding, and high-resolution imaging and reconstruction of the pattern of cortical columns. We present the dependence of the performance of each approach on the parameters of the imaged pattern as well as those of the data acquisition. In addition, we predict voxel sizes that optimize fMRI of cortical columns under various scenarios. We found that all measures associated with multivariate detection and decoding could be approximately calculated from a measure we termed “multivariate contrast-to-noise ratio” (mv-CNR), which is a function of the contrast-to-noise ratio (CNR) and number of voxels. Furthermore, mv-CNR implied that the optimal voxel width for detection and decoding is independent of changes in response amplitude, SNR and imaged volume that are not caused by changes in voxel size. For regular patterns, optimal voxel widths for detection, decoding and imaging/reconstructing the pattern of cortical columns were approximately half the main cycle length of the organization. Optimal voxel widths for irregular patterns were less dependent on the main cycle length, and differed between univariate detection, multivariate detection and decoding, and reconstruction. We compared the effects of different factors of Gradient Echo fMRI at 3 Tesla (T), Gradient Echo fMRI at 7T, and Spin-Echo fMRI at 7T on the detection, decoding, and reconstruction measures considered and found that in all cases the width of the fMRI point-spread had the most significant effect. In contrast, different response amplitudes and noise characteristics played a relatively minor role. We recommend specific voxel widths for optimal univariate detection, for multivariate detection and decoding, and for high-resolution imaging of cortical columns under these three data-acquisition scenarios. Our study supports the planning, optimization, and interpretation of high-resolution fMRI of cortical columns and the decoding of information conveyed by these columns.

Original languageEnglish (US)
Pages (from-to)67-99
Number of pages33
StatePublished - Jan 1 2018

Bibliographical note

Funding Information:
We thank Jiachen Liang and Dante Louie for editing the manuscript. This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada (AS, NSERC Discovery grants RGPIN 375457-09 and RGPIN-2015-05103 ).


  • BOLD
  • Blood oxygenation level dependent
  • Cortical columns
  • Cortical maps
  • Decoding
  • Gradient-Echo functional MRI
  • High-resolution functional MRI
  • MVPA
  • Multivariate pattern analysis
  • Point-spread function
  • Spin-Echo functional MRI
  • Ultra-high field MRI

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