Computational protocol: Functional Imaging Reveals Movement Preparatory Activity in the Vegetative State

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Protocol publication

[…] We assessed the degree of cortical and subcortical atrophy using a visual rating scale based upon that developed by Galton et al. (). Briefly, we first defined atrophy levels from 0 to 4 using T1-3D anatomical images (0 = no atrophy, 1 = very low, 2 = mild, 3 = severe, and 4 = highly severe atrophy) in a group of 12 patients with neurodegenerative disorders, and applied the scale to the VS patients included in this study (see Table ). Patients’ T1-weighted images were assessed by two experienced raters (Tristan Andres Bekinschtein and Facundo Francisco Manes) who were blind to the patient's clinical history. Images were aligned and inspected using the free viewing software MRIcro for Windows ( with no further transformations. [...] Functional images were pre-processed and analyzed using Statistical Parametric Mapping (SPM2, Wellcome Department of Cognitive Neurology, London, UK). Pre-processing steps included realignment and reslicing. Whole-brain univariate analyses were carried out for each individual subject by using a general lineal model for each voxel following a fixed-effects model. Data for each subject was modeled with a boxcar convolved with a synthetic hemodynamic response function. Movement parameters were entered as additional predictors in the general lineal model. A statistical voxel threshold of p < 0.001 (uncorrected for multiple comparisons) with a minimum of three contiguous voxels was used for whole-brain analysis for three reasons: first, BOLD responses in this patient group are known to be diminished (Boly et al., ; Laureys et al., ), second, a relatively low magnetic field was used for this study (1.5 T), third, unlike most fMRI studies, in this study we sought to identify motor preparation responses at the single-subject level, not at a group level. In addition, region of interest (ROI) statistical analysis (small volume correction) was carried out to further assess the significance of premotor voxels using a more conservative criterion (Poldrack et al., ). Six different premotor ROIs were drawn following Picard and Strick's ()functional distinction using the MarsBar SPM toolbox (Brett et al., ). These are depicted in Figure , and correspond to right and left dorsal premotor cortex (PMd; this region lies on the most posterior part of the precentral gyrus), right and left pre-premotor cortex (pre-PMd, this region lies over the most anterior part of the precentral gyrus), supplementary motor area (SMA) proper and pre-SMA. MarsBar averages the beta values resulting from fitting the BOLD signal with the model for all voxels in each ROI, runs the GLM on this average and corrects for the total number of ROIs evaluated (n = 6). The ROI threshold was set at p < 0.05 corrected for multiple comparisons. t Values were adjusted by number or ROIs, defined a priori based on specific predictions drawn on our hypothesis stated in the introduction, not by total number of evaluated contrasts.Functional images were pre-processed, registered to their corresponding T1 and manually normalized to the MNI anatomical template (MNI-152) using a linear transformation algorithm. ROIs were drawn on the MNI 152 template and superimposed onto each subject's structural image; final adjustments were performed manually to account for variability in gyri and sulci using the precentral gyrus, postcentral gyrus, and the central sulcus as anatomical landmarks. […]

Pipeline specifications

Software tools MRIcro, Picard
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Injury, Chronic