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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    • "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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    ABSTRACT: Perceptions of sensation and pain in healthy people are believed to be the net result of sensory input and descending modulation from brainstem and cortical regions depending on emotional and cognitive factors. Here, the influence of attention on neural activity in the spinal cord during thermal sensory stimulation of the hand was investigated with functional magnetic resonance imaging by systematically varying the participants' attention focus across and within repeated studies. Attention states included (1) attention to the stimulus by rating the sensation and (2) attention away from the stimulus by performing various mental tasks of watching a movie and identifying characters, detecting the direction of coherently moving dots within a randomly moving visual field and answering mentally-challenging questions. Functional MRI results spanning the cervical spinal cord and brainstem consistently demonstrated that the attention state had a significant influence on the activity detected in the cervical spinal cord, as well as in brainstem regions involved with the descending analgesia system. These findings have important implications for the detection and study of pain, and improved characterization of the effects of injury or disease.
    Magnetic Resonance Imaging 01/2011; 29(1):9-18. DOI:10.1016/j.mri.2010.07.012 · 2.09 Impact Factor
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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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    ABSTRACT: Demonstrations of the possibility of obtaining functional information from the spinal cord in humans using functional magnetic resonance imaging (fMRI) have been growing in number and sophistication, but the technique and the results that it provides are still perceived by the scientific community with a greater degree of scepticism than fMRI investigations of brain function. Here we review the literature on spinal fMRI in humans during voluntary movements and somatosensory stimulation. Particular attention is given to study design, acquisition and statistical analysis of the images, and to the agreement between the obtained results and existing knowledge regarding spinal cord anatomy and physiology. A striking weakness of many spinal fMRI studies is the use of small numbers of subjects and of time-points in the acquired functional image series. In addition, spinal fMRI is characterised by large physiological noise, while the recorded functional responses are poorly characterised. For all these reasons, spinal fMRI experiments risk having low statistical power, and few spinal fMRI studies have yielded physiologically relevant information. Thus, while available evidence indicates that spinal fMRI is feasible, we are only approaching the stage at which the technique can be considered to have been rigorously established as a viable means of noninvasively investigating spinal cord functioning in humans.
    Magnetic Resonance Imaging 10/2010; 28(8):1216-24. DOI:10.1016/j.mri.2010.05.001 · 2.09 Impact Factor
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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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    ABSTRACT: Cervical spinal cord displacements have recently been measured in relation to the cardiac cycle, substantiating that cord motion in this region reduces both the sensitivity and reproducibility of functional magnetic resonance imaging of the spinal cord (spinal fMRI). Given the ubiquitous and complex nature of this motion, cardiac gating alone is not expected to sufficiently remove these errors, whereas current modeling approaches for spin-echo methods are not specific to motion artifacts, potentially eliminating function-related data along with components of motion-related noise. As such, we have developed an alternative approach to spinal cord motion-compensation, using retrospective spinal cord motion time-course estimates (RESPITE) to forecast a small number of physiological noise regressors. These are generated from the principal components of spinal cord motion, as well as subject-specific cardiac data, and are subsequently included in a general linear model (GLM) analysis. With this approach, the components of motion-related signal fluctuation are modeled, along with functionally-relevant signal changes (i.e., those components fitting the stimulus paradigm), to account for the effects of spinal cord and cerebrospinal fluid (CSF) motion in a thorough, yet discerning, manner. By analyzing 100 previously acquired half-Fourier turbo spin-echo (HASTE) spinal fMRI data sets, along with a collection of null-task data, we show that the implementation of RESPITE reduces the occurrence of both type I (false-positive) and type II (false negative) errors, effectively increasing the specificity (5-6%) and sensitivity (15-20%) to neuronal activity.
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