Spatial normalization, bulk motion correction and coregistration for functional magnetic resonance imaging of the human cervical spinal cord and brainstem

Centre for Neuroscience Studies, Queen's University, Kingston, Ontario, Canada K7L 3N6.
Magnetic Resonance Imaging (Impact Factor: 2.09). 08/2008; 26(6):809-14. DOI: 10.1016/j.mri.2008.01.038
Source: PubMed


Functional magnetic resonance imaging (fMRI) of the cortex is a powerful tool for neuroscience research, and its use has been extended into the brainstem and spinal cord as well. However, there are significant technical challenges with extrapolating the developments that have been achieved in the cortex to their use in the brainstem and spinal cord. Here, we develop a normalized coordinate system for the cervical spinal cord and brainstem, demonstrating a semiautomated method for spatially normalizing and coregistering fMRI data from these regions. fMRI data from 24 experiments in eight volunteers are normalized and combined to create the first anatomical reference volume, and based on this volume, we define a standardized region-of-interest (ROI) mask, as well as a map of 52 anatomical regions, which can be applied automatically to fMRI results. The normalization is demonstrated to have an accuracy of less than 2 mm in 93% of anatomical test points. The reverse of the normalization procedure is also demonstrated for automatic alignment of the standardized ROI mask and region-label map with fMRI data in its original (unnormalized) format. A reliable method for spatially normalizing fMRI data is essential for analyses of group data and for assessing the effects of spinal cord injury or disease on an individual basis by comparing with results from healthy subjects.

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Available from: Chase R Figley, Nov 11, 2015
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    • "The individual results are expressed as the significance (T value) that β 1 /β 0 is not equal to zero, for each voxel spanned by the image data. The results were then reformatted and normalized to a consistent coordinate space, defined for the brainstem and spinal cord, to facilitate group comparisons [35]. Briefly, the normalization procedure consists of interpolating the image data to 1- mm cubic voxels and reslicing the volume into axial sections every 1 mm along a manually-defined reference line along the anterior edge of the spinal cord in a mid-line sagittal slice. "
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    • "Whereas some early studies (e.g., Madi et al. [48]) used blurring kernels of several millimetres, more recent publications have tended to forego spatial smoothing or adopt anisotropic smoothing favouring the rostro-caudal axis of the cord. For sagittal images, Stroman et al. have introduced a process of shifting voxels along the dorsoventral axis so that the midline, ventral edge of the spine is straight as a means to improve subsequent anisotropic smoothing [44] "
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    • "These data are then spatially normalized and co-registered to a spinal cord reference volume (Stroman et al., 2008a), allowing region-ofinterest (ROI) analysis, and enabling comparisons across a group (or groups) of subjects. By means of an ROI mask, the software also permits data from different regions of the cord, brainstem, and/or surrounding anatomy (i.e., CSF, vertebrae, etc.) to be included or excluded from further analysis. "
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