Computational protocol: Processing of pitch and location in human auditory cortex during visual and auditory tasks

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Protocol publication

[…] Functional magnetic resonance imaging data were acquired with a 3 T MAGNETOM Skyra scanner (Siemens Healthcare, Erlangen, Germany) using a standard 20-channel head-neck coil. First, high-resolution anatomical image (sagittal slices, slice thickness 1.0 mm, in-plane resolution 1.0 mm × 1.0 mm) was acquired. Second, functional images (GE-EPI; TR 2070 ms, TE 30 ms, flip angle 78°, voxel matrix 96 × 96, FOV 18.9 cm × 18.9 cm, slice thickness 2.0 mm with no gap, in-plane resolution 2.0 mm × 2.0 mm, 27 slices) were acquired in two 30 min runs with a short break in between. The middle EPI slices were aligned along the Sylvian fissures based on the anatomical image. The imaged area covered the superior temporal lobe, insula, and most of the inferior parietal lobe in both hemispheres (Figure ). Finally, a T2-weighted image using the same imaging slices but with denser in-plane resolution was acquired (TR 4500, TE 100 ms, voxel matrix 256 × 240, FOV 24 cm, slice thickness 2.0 mm).FreeSurfer was used for reconstruction of cortical surfaces and coregistration (version 5.3.0). Functional data were motion-corrected, resampled to the standard cortical surface, and surface-smoothed (5 mm FWHM). Global vertex-wise analysis was performed in surface space using FILM (FMRIB’s Improved Linear Model; FSL version 5.0.7). Each task (18) was included as a separate explanatory variable, and the hemodynamic response function was modeled with a gamma function (mean lag 6 s, SD 3 s) and its temporal derivative. A second level analysis using fixed effects combined the data from the two runs. Third level group analysis was performed using FSL’s PALM (Permutation Analysis of Linear Models; version alpha26, ). Parameter estimates (from second level analysis) were compared using repeated-measures ANOVAs and t-tests. Significance was assessed by permutation inference (10000 permutations). Correction for multiple comparisons was performed using cluster-mass correction (cluster forming threshold Z > 2.3). For visualization, results were converted to 2D using Mollweide projection (Python libraries matplotlib and basemap). […]

Pipeline specifications

Software tools FreeSurfer, matplotlib
Applications Miscellaneous, Functional magnetic resonance imaging
Organisms Homo sapiens