Computational protocol: Voluntary saccade inhibition deficits correlate with extended white-matter cortico-basal atrophy in Huntington's disease

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Protocol publication

[…] T1 images were analyzed through the Voxel-based morphometry technique implemented on FMRIB Software Library (FSL) (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM). First, voxels that did not belong to the images of the cerebral tissue were eliminated using (Brain Extraction Tool) BET software. Afterwards, segmentation was done according to the type of tissue sampled (grey-matter, white-matter and cerebrospinal fluid) using FAST4. The images corresponding to the grey-matter were aligned to the MNI152 standard space by means of a linear followed by a non-linear co-registration in order to obtain optimal co-registration. The average of these co-registered images was obtained to generate the specific standard for this study. The grey-matter images were co-registered to this specific standard through a non-linear co-registration and local changes in expansion or contraction were corrected by modulation. A smoothing process was applied with a Gaussian isotropic kernel with a sigma of 4 mm. An independent two-sample t-test was applied through the general linear model correcting for multiple comparisons using randomized permutation methods (n = 10,000). We chose the appropriate smoothing (sigma 4 mm) for the Threshold-Free Cluster Enhancement (TFCE) based analysis. The family-wise error (FWE) was controlled and only corrected 1 – p values ≤ 0.095 were accepted. […]

Pipeline specifications

Software tools FSL, BET
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Huntington Disease, Neurodegenerative Diseases