Reliable 3D mapping of ocular dominance columns in humans using GE-EPI fMRI at 7 T

Poster No:


Submission Type:

Abstract Submission 


Daniel Haenelt1,2, Nikolaus Weiskopf1, Roland Mueller1, Shahin Nasr3,4, Jonathan Polimeni3,4, Roger Tootell3,4, Martin Sereno5, Robert Trampel1


1Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, 2International Max Planck Research School on Neuroscience of Communication: Function, Structure, and Plasticity, Leipzig, Germany, 3Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Boston, USA, 4Department of Radiology, Harvard Medical School, Boston, USA, 5Department of Psychology, College of Sciences, San Diego State University, San Diego, USA



Since the discovery of the BOLD effect, detection of ocular dominance columns (ODCs) in primary visual cortex (V1) served as a benchmark for high-precision functional magnetic resonance imaging (fMRI) (Menon et al., 1997; Dechent and Frahm 2000; Cheng et al., 2001; Yacoub et al., 2007). Although gradient-echo (GE) echo-planar imaging (EPI) is often used at lower field strengths, the applicability for high-resolution fMRI at higher field strengths is still under debate because of its inherent sensitivity to large draining veins (Polimeni et al., 2010). To counteract the loss of specificity, it was recently suggested to only sample far away from the pial surface when using GE-EPI (Nasr et al., 2016; Polimeni et al., 2017). Here, we assessed whether differential ocular dominance responses can be resolved using GE-EPI with different isotropic resolutions (0.8 mm and 1.0 mm) and how the corresponding BOLD signal is distributed across the cortex.


Experiments were performed on a 7 T whole-body MR scanner (Siemens Healthineers, Germany) using a 32 channel phased array head RF coil (Nova Medical Inc, USA). The study was carried out with ethical approval from the local Ethics Committee, and informed consent was obtained. One participant was invited to multiple scanning sessions on different days. In the first session, for structural and functional reference a whole-brain T1-weighted data set (MP2RAGE; Marques et al., 2010) and a retinotopic map (Sereno et al., 2013) were acquired. In the remaining four sessions each 43 min in length, ODCs were localized using a differential paradigm with alternating visual stimulation of either left or right eye by moving sparse random dot stereograms viewed through anaglyph goggles (Nasr et al., 2016). For acquisition, the slice group was positioned in a coronal fashion covering early visual areas. Two different GE-EPI protocols were used in sessions 1+2 and 3+4, respectively: TR = 3000 ms/2000 ms, TE = 24 ms/21 ms, FA = 78°/66°, number of slices = 50/40, voxel size = (0.8 mm)³/(1.0 mm)³, GRAPPA = 3, partial Fourier = 6/8. SPM12 was used for GLM analysis without spatial smoothing. The cortex was segmented using FreeSurfer. Resulting surface meshes were up-sampled to an average edge length of 0.3 mm, and the cortex was divided into 10 layers using the equi-volume approach (Waehnert et al., 2014). A patch on the inflated surface was cut and flattened. The flattened patch was sampled onto a regular grid with isotropic 0.25 mm pixel size. Regular patches of each layer were stacked together and activation maps (left eye > right eye) were sampled onto that grid. Because ODCs are not directly accessible with MRI, we performed a test-retest analysis in two representative ROIs and measured the vertex-wise correlation between sessions, expecting only a high correlation within the stimulated visual field of V1 (see caption of fig. 2 for further explanation).


Figure 1 shows ODCs on the inflated surface of the right hemisphere for single sessions. The expected stripe-like structure conforming to ODCs in tangential direction of the cortex can be identified in each session. Similar results were found on the left hemisphere (not shown). Additionally, the same activation maps are shown on a regular grid in cross section for all sessions (Fig. 1b, bottom). The columnar pattern is seen in each cross section with blurring towards the pial surface. Figure 2 shows the reliability of the activation pattern analyzed as vertex-wise correlation between sessions in two different ROIs. The correspondence in more posterior parts of V1 is apparent.
Supporting Image: figure1_bb.png
Supporting Image: figure2_bb.png


ODCs can be mapped robustly using GE-EPI with isotropic 0.8 mm and 1.0 mm in line with Nasr et al. (2016). In all maps, blurring in the tangential plane towards the pial surface is evident. This demonstration of functionally-based fine structures (ODCs) with high resolution can help future research to quantify the cortical depth dependent vascular blurring in GE-EPI and other sequences.

Imaging Methods:


Modeling and Analysis Methods:

Methods Development 2


Anatomy and Functional Systems

Perception and Attention:

Perception: Visual


Cortical Columns
Cortical Layers

1|2Indicates the priority used for review

My abstract is being submitted as a Software Demonstration.


Please indicate below if your study was a "resting state" or "task-activation” study.


Healthy subjects only or patients (note that patient studies may also involve healthy subjects):

Healthy subjects

Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.


Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

Not applicable

Please indicate which methods were used in your research:

Functional MRI
Structural MRI

For human MRI, what field strength scanner do you use?


Which processing packages did you use for your study?

Free Surfer

Provide references using author date format

Cheng K. (2001), 'Human ocular dominance columns as revealed by high-field functional magnetic resonance imaging', Neuron, vol. 32, no. 2, pp. 359-374.
Dechent, P. (2000), 'Direct mapping of ocular dominance columns in human primary visual cortex', Neuroreport, vol. 11, no. 14, pp. 3247-3249.
Marques, J. P. (2010), 'MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field', Neuroimage, vol. 49, no. 2, pp. 1271-1281.
Menon, R. S. (1997), 'Ocular dominance in human V1 demonstrated by functional magnetic resonance imaging', Journal of Neurophysiology, vol. 77, no. 5, pp. 2780–2787.
Polimeni, J. R. (2010), 'Laminar analysis of 7T BOLD using an imposed spatial activation pattern in human V1', Neuroimage, vol. 52, no. 4, pp. 1334-1346.
Polimeni, J. R. (2017), 'Analysis strategies for high-resolution UHF-fMRI data', Neuroimage, vol. 168, pp. 296-320.
Nasr, S. (2016), 'Interdigitated color- and disparity-selective columns within human visual cortical areas V2 and V3, Journal of Neuroscience, vol. 36, no. 6, 1841-1857.
Sereno, M. I. (2013), 'Mapping the human cortical surface by combining quantitative T1 with retinotopy', Cerebral Cortex, vol. 23, no. 9, 2261-2268.
Waehnert, M. D. (2014), 'Anatomically motivated modeling of cortical laminae', Neuroimage, vol. 93, no. 2, pp. 210-220.
Yacoub, E. (2007), 'Robust detection of ocular dominance columns in humans using Hahn Spin Echo BOLD functional MRI at 7 Tesla', Neuroimage, vol. 37, no. 4, 1161-1177.