Computational protocol: Brain mapping for long-term recovery of gait after supratentorial stroke

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Protocol publication

[…] For the voxel-based lesion symptom mapping (VLSM) analysis, we performed the following procedures. First, the lesion of each patient was drawn on the high-resolution T1-weighted image in the native space using MRIcro software ( Second, images of 22 patients with lesions in the right hemisphere were flipped to locate the lesion area of all patients within the left hemisphere to create a lesion-overlapping map and conduct statistical comparisons. Third, each individual's T1-weighted image and native-space lesion image were nonlinearly transformed to the standardized Montreal Neurological Institute space using SPM12 ( Lastly, VLSM uses the lesion status at each voxel as a grouping variable, and then it compares the lesioned and nonlesioned groups for all dependent variables using a custom MATLAB script. At each voxel, we performed an independent sample t-test to identify differences in gait parameters between the lesion and nonlesion regions. Significant brain regions were determined at a threshold of cluster-level corrected P < .05, which corresponded to a voxel-level threshold P < .005 and cluster size k > 21 voxels. The cluster size was determined through a Monte Carlo simulation using AFNI's 3dClustSim program ( with 10,000 iterations.[] Analysis between patients’ and normal control group was performed using an independent t-test. Significance level was P < .05. […]

Pipeline specifications

Software tools MRIcro, SPM, AFNI
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Diseases, Stroke