Reliable 3D mapping of ocular dominance columns in humans using GE-EPI fMRI at 7 T
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.
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.
BOLD fMRI 1
Modeling and Analysis Methods:
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HIGH FIELD MR
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Dechent, P. (2000), 'Direct mapping of ocular dominance columns in human primary visual cortex', Neuroreport, vol. 11, no. 14, pp. 3247-3249.
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