Computational protocol: Measurement of cortical thickness asymmetry in carotid occlusive disease

Similar protocols

Protocol publication

[…] Imaging was performed on 3T Philips Achieva scanners in the medical centers of Columbia University (patients) and Leiden University (healthy controls). A high-resolution 3D T1-weighted (MPRAGE) image was acquired on each participant with the following parameters: TE = 3 ms, TR = 6.7 ms, in plane resolution 0.9 × 0.9 mm2, slice thickness = 0.9 mm, 120 slices. An in-house SPM12 (Wellcome Trust Centre for Neuroimaging, London, UK) based script was used to flip the orientation of the images such that they were available in both neurological and radiological orientations. This was done to test for any orientation bias in Freesurfer's performance of cortical thickness estimation.Volumetric tissue segmentation and inference of cortical structure were obtained from each patient's MPRAGE (neurological and radiological orientation, independently) using the Freesurfer software ().Briefly, the Freesurfer approach involved: (1) removal of non-tissue voxels using a hybridized watershed/surface deformation algorithm (), (2) computation of forward and inverse transforms into Talairach space, (3) volumetric segmentation of subcortical white matter and deep gray matter structures (, ), (4) intensity normalization (), (5) tessellation of the boundary between gray and white matter, (6) automated topology correction (, ), and (7) surface deformation, which is conducted along intensity gradients such that transitional borders are positioned along the greatest shift in signal intensity aligned with the border to the next tissue class (, , ).Following the registration to a spherical brain atlas utilizing cortical folding patterns of subjects to match cortical geometry across subjects (), the cerebral cortex was parcellated into different regions based on the structure of the gyri and sulci (, ). With both the inner and outer cortical surfaces identified and isolated, the cortical thickness of a subject was calculated as the Euclidean distance between the two surfaces ().The cortical thickness maps are created through the use of spatial intensity gradients across tissue classes and are therefore largely invariant to absolute signal intensity.Based on the parcellation results, regions of interest were selected for the cortical thickness map of the primary motor cortex (M1) and primary visual cortex (V1). Data from these ROIs were used to compute cortical thickness and volume, which were subsequently used in the analysis described below. […]

Pipeline specifications

Software tools SPM, FreeSurfer
Application Neuroimaging analysis
Diseases Muscular Diseases