Computational protocol: A role of the human thalamus in predicting the perceptual consequences of eye movements

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Protocol publication

[…] Imaging and lesion reconstruction was identical to Liebermann et al. (). In brief, structural imaging was performed on a clinical whole-body scanner (Magnetom Vision, Siemens) at 1.5 T. For reconstruction of lesions, a three-dimensional dataset was acquired, using a magnetization prepared rapid acquisition gradient-echo imaging sequence (MPRAGE, isotropic resolution 1 mm). To screen for additional extra- and intrathalamic lesions at the time of testing, axial images of the whole brain and coronal images of the thalamic region were acquired using a T2-weighted turbo inversion recovery magnitude sequence (whole brain and thalamus, voxel-size 0.91 × 0.9 × 5 mm and 0.95 × 0.9 × 2 mm, respectively). High-resolution imaging revealed no further lesions except for single lacunar lesions in four patients [left cerebellum, lobule VI (patient P6) and lobule VIIIb (patient P3), right cerebellum, lobule VI (patient P5), and genu of corpus callosum (patient P8)]. In addition, the thalamic lesion of one patient extended slightly into the right hypothalamus (patient P13).Individual brain scans were spatially normalized using MATLAB (The MathWorks, Natick, MA, USA) and the Statistical Parametric Mapping package (SPM5, Wellcome Department of Imaging Neuroscience, London, http://www.fil.ion.ucl.ac.uk/spm). Individual MRI data sets were normalized to a T1 Montreal Neurological Institute (MNI) template provided with SPM by using the unified segmentation and normalization function. This method has recently been demonstrated to provide reliable normalization of focally lesioned brains to template images (Crinion et al., ), although cost function masking might still be recommended for larger lesions (Andersen et al., ). For identification of affected thalamic nuclei in individual patients, lesions were co-registered to an atlas of the human thalamus (Morel, ). Coronal reconstructions from MRI data sets were evaluated against corresponding atlas plates. Relative lesion extent for a given thalamic nucleus was rated in three increments (less than 1/3, between 1/3 and 2/3, more than 2/3 of nucleus volume affected, see Figure ). Lesion overlap and subtraction plots (Rorden and Karnath, ) were generated on a group level for further lesion-to-symptom mapping. For this analysis, lesions were manually traced in normalized three-dimensional space with MRIcron software (version as of December 2012, www.mccauslandcenter.sc.edu/mricro/mricron/index.html). Estimation of lesion volume and lesion overlap and subtraction analyses (Rorden and Karnath, ) were conducted with resulting volumes of interest (VOIs) in MRIcron. For further statistical analysis we used non-parametric voxel-based lesion-symptom mapping as implemented in NPM, which is part of the MRIcron software package. Only voxels that were lesioned in at least 2 patients were included in this analysis. […]

Pipeline specifications

Software tools SPM, MRIcron
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Ocular Motility Disorders, Vaginal Discharge, Stroke