Computational protocol: Responses in early visual areas to contour integration are context dependent

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Protocol publication

[…] Functional data was motion corrected using Analysis of Functional NeuroImages software (AFNI; Cox, ), with reference to the volume right before a within-session fieldmap image. The motion-corrected data was unwarped using FSL FUGUE to correct distortions introduced by magnetic field inhomogeneities (Smith et al., ). High-pass filtering was also applied to the functional localizers data: temporal frequencies below four cycles per run were removed. The preprocessed functional data were then aligned to anatomical reference data using mrAlign implemented in Matlab (MathWorks, Inc.; http://gru.stanford.edu/doku.php/mrTools/overview).ROIs were defined based on both retinotopic visual areas and functional localizers for each observer. Three repetitions of the functional localizers were averaged to define the ROIs responding to the target (tg) or background (bkgd) regions. For each voxel coherence (unsigned correlation, computed in the Fourier domain as the amplitude of the stimulus-related Fourier component normalized by the square root of the integrated power spectrum) with a sinusoid at the block-alternation frequency, 10 cycles per run, was calculated in the averaged localizer scans (Bandettini, Jesmanowicz, Wong, & Hyde, ; Engel et al., ). The voxels with coherence exceeding 0.30 were included in the ROIs. The voxels in phase with the target representation were assigned to target ROIs (tgROIs), and the voxels in phase with the background representation were assigned to background ROIs (bkgdROIs). ROIs were initially defined on a flattened cortical surface, where V1, V2, and V3 boundaries could be used to identify the ROIs in different visual areas. Selected voxels were translated to the in-plane space for further refinement to include only contiguous clusters of visually responsive voxels, and the defined ROIs were then exported as a binary mask in the space of the functional data. Six ROIs were defined for each observer: tgV1, tgV2, tgV3, bkgdV1, bkgdV2, and bkgdV3. […]

Pipeline specifications

Software tools AFNI, VISTASOFT
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens