Computational protocol: Nonlinear population receptive field changes in human area V5/MT+ of healthy subjects with simulated visual field scotomas

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Protocol publication

[…] Functional and structural MRI experiments were performed at the Max Planck Institute for Biological Cybernetics, Tuebingen, Germany using a 3.0 Tesla high-speed echo-planar imaging device (Trio, Siemens Ltd., Erlargen, Germany) with a quadrature head coil. At least two T1-weighted anatomical volumes were acquired for each subject with a three-dimensional magnetization prepared rapid acquisition gradient echo (T1 MPRAGE scan) and averaged following alignment to increase signal to noise ratio (matrix size = 256 × 256, voxel size = 1 × 1 × 1 mm3, 176 partitions, flip angle = 9°, repetition time [TR] = 1900 ms, echo time [TE] = 2.26 ms, TI = 900 ms). Blood oxygen level dependent (BOLD) image volumes were acquired using gradient echo sequences of 28 contiguous 3 mm-thick slices covering the entire brain (repetition time [TR] = 2000 ms, echo time [TE] = 40 ms, matrix size = 64 × 64, voxel size = 3 × 3 × 3 mm3, flip angle = 90°).At least 5 functional scans were acquired for each subject, consisting of 195 image volumes, the first 3 of which were discarded. The functional images were corrected for motion in between and within scans (). The functional images were aligned to the high-resolution anatomical volume using a mutual information method () where the resampled time series values in the volume are spatially interpolated relative to the nearest functional voxels. All subsequent analysis was performed in the interpolated data. However, we took care that this does not affect the retinotopic maps obtained and the statistical comparisons that are performed, because the interpolation method we used does not distort the generated time series and the comparisons we made were between different groups of subjects rather than between different numbers of voxels. Preprocessing steps were performed in MATLAB using the mrVista toolbox (http://white.stanford.edu/software/). [...] Subjects were presented with moving square-checkerboard bars (100% contrast) through MRI compatible digital goggles (VisuaStim, Resonance Technology Company, Inc., Northridge, CA, USA; 30° horizontal and 22.5° vertical field of view, 800×600 resolution, min luminance = 0.3 cd/m2 and max luminance = 12.2 cd/m2). The stimulus was presented within a circular aperture with a radius of 11.25° around the fixation point. The bar width was 1.875° and travelled sequentially in 8 different directions, moving by a step half of its size (0.9375°) every image volume acquisition (TR = 2 seconds). Stimuli were generated using Psychtoolbox () and an open toolbox (VISTADISP) in MATLAB (The Mathworks, Inc.). The subjects’ task was to fixate a small dot in the center of the screen (radius: 0.0375°; 2 pixels) and respond to the color change by pressing a button. The color was changing randomly with a frequency of one every 6.25 seconds. An infrared eye tracker was used to record eye movements inside the scanner (iView XTM, SensoMotoric Instruments GmbH) (). For two of the subjects (S4–S5) the eye movements under the full field stimulus presentation were not recorded due to technical problems. However, they performed a challenging detection task at fixation and their performance was always >95% correct. […]

Pipeline specifications

Software tools VISTASOFT, VistaDisp
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Retinal Diseases, Angelman Syndrome