This material is based upon work supported by the National Science Foundation under Grant BCS 1063774.

1. Polar-angle Topography Stimulus and Psychophysics
To obtain a polar-angle retinotopic map in the SC, we use a 90&deg; wedge of moving dots as the stimulus (eccentricity 2-9&deg; of visual angle, mean dot-speed 4&deg; / sec) (Fig. 1). It is known that activity in the SC is enhanced by applying covert attention5, hence we use an attention task in our paradigm to increase available signal. On each 2 s trial, subjects are instructed to covertly attend to the entire wed...

<ol>
	<li>Katyal, S., Zughni, S., Greene, C., Ress, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Topography+of+covert+visual+attention+in+human+superior+colliculus.">Topography of covert visual attention in human superior colliculus.</a> Journal of Neurophysiology. 104, 3074-3083 (2010).</li><li>Yushkevich, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=User-guided+3D+active+contour+segmentation+of+anatomical+structures:+significantly+improved+efficiency+and+reliability.">User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.</a> NeuroImage. 31, 1116-1128 (2006).</li><li>Xu, G., Pan, Q., Bajaj, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discrete+Surface+Modeling+Using+Partial+Differential+Equations.">Discrete Surface Modeling Using Partial Differential Equations.</a> Computer Aided Geometric Design. 23, 125-145 (2006).</li><li>Ress, D., Glover, G. H., Liu, J., Wandell, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laminar+profiles+of+functional+activity+in+the+human+brain.">Laminar profiles of functional activity in the human brain.</a> NeuroImage. 34, 74-84 (2007).</li><li>Schneider, K. A., Kastner, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+sustained+spatial+attention+in+the+human+lateral+geniculate+nucleus+and+superior+colliculus.">Effects of sustained spatial attention in the human lateral geniculate nucleus and superior colliculus.</a> J. Neurosci. 29, 1784-1795 (2009).</li><li>Glover, G. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+analytic+spiral+K-space+algorithm.">Simple analytic spiral K-space algorithm.</a> Magn. Reson. Med. 42, 412-415 (1999).</li><li>Glover, G. H., Lai, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-navigated+spiral+fMRI:+interleaved+versus+single-shot.">Self-navigated spiral fMRI: interleaved versus single-shot.</a> Magn. Reson. Med. 39, 361-368 (1998).</li><li>Nestares, O., Heeger, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Robust+multiresolution+alignment+of+MRI+brain+volumes.">Robust multiresolution alignment of MRI brain volumes.</a> Magn. Reson. Med. 43, 705-715 (2000).</li><li>Engel, S. A., Glover, G. H., Wandell, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retinotopic+organization+in+human+visual+cortex+and+the+spatial+precision+of+functional+MRI.">Retinotopic organization in human visual cortex and the spatial precision of functional MRI.</a> Cereb. Cortex. 7, 181-192 (1997).</li><li>Schneider, K. A., Kastner, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visual+responses+of+the+human+superior+colliculus:+a+high-resolution+functional+magnetic+resonance+imaging+study.">Visual responses of the human superior colliculus: a high-resolution functional magnetic resonance imaging study.</a> Journal of Neurophysiology. 94, 2491-2503 (2005).</li><li>Cynader, M., Berman, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Receptive-field+organization+of+monkey+superior+colliculus.">Receptive-field organization of monkey superior colliculus.</a> Journal of Neurophysiology. 35, 187-201 (1972).</li><li>Robinson, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Eye+movements+evoked+by+collicular+stimulation+in+the+alert+monkey.">Eye movements evoked by collicular stimulation in the alert monkey.</a> Vision Research. 12, 1795-1808 (1972).</li><li>Schreiner, C. E., Langner, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laminar+fine+structure+of+frequency+organization+in+auditory+midbrain.">Laminar fine structure of frequency organization in auditory midbrain.</a> Nature. 388, 383-385 (1997).</li><li>Baumann, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Orthogonal+representation+of+sound+dimensions+in+the+primate+midbrain.">Orthogonal representation of sound dimensions in the primate midbrain.</a> Nature Neuroscience. 14, 423-425 (2011).</li><li>Malmierca, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+discontinuous+tonotopic+organization+in+the+inferior+colliculus+of+the+rat.">A discontinuous tonotopic organization in the inferior colliculus of the rat.</a> J. Neurosci. 28, 4767 (2008).</li><li>Bender, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retinotopic+organization+of+macaque+pulvinar.">Retinotopic organization of macaque pulvinar.</a> Journal of Neurophysiology. 46, 672 (1981).</li><li>Grieve, K. L., Acuña, C., Cudeiro, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+primate+pulvinar+nuclei:+vision+and+action.">The primate pulvinar nuclei: vision and action.</a> Trends in Neurosciences. 23, 35-39 (2000).</li><li>Rodriguez-Oroz, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+subthalamic+nucleus+in+Parkinson's+disease:+somatotopic+organization+and+physiological+characteristics.">The subthalamic nucleus in Parkinson's disease: somatotopic organization and physiological characteristics.</a> Brain. 124, 1777 (2001).</li><li>Romanelli, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microelectrode+recording+revealing+a+somatotopic+body+map+in+the+subthalamic+nucleus+in+humans+with+Parkinson+disease.">Microelectrode recording revealing a somatotopic body map in the subthalamic nucleus in humans with Parkinson disease.</a> Journal of Neurosurgery. 100, 611-618 (2004).</li><li>DeLong, M. R., Crutcher, M. D., Georgopoulos, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Primate+globus+pallidus+and+subthalamic+nucleus:+functional+organization.">Primate globus pallidus and subthalamic nucleus: functional organization.</a> Journal of Neurophysiology. 53, 530 (1985).</li><li>Houeto, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acute+deep-brain+stimulation+of+the+internal+and+external+globus+pallidus+in+primary+Dystonia+functional+mapping+of+the+pallidum.">Acute deep-brain stimulation of the internal and external globus pallidus in primary Dystonia functional mapping of the pallidum.</a> Archives of Neurology. 64, 1281-1286 (2007).</li></ol>

No conflicts of interest declared.

Our acquisition and data-analysis techniques enable the measurement of neural activity in subcortical human brain structures at high resolution (1.2 mm voxels). The 3-shot spiral acquisition reduces the physiological noise that is particularly detrimental to fMRI measurements around the midbrain. In addition, our laminar segmentation of the tissue allows us to perform depth averaging of the data that helps improve the SNR. We have used these methods to show precise polar-angle topographic maps of visual stimulation and c...

high-resolution functional magnetic resonance imaging methods for human midbrain

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon measuring activity on the surface of cerebral cortex rather than in subcortical regions such as midbrain and brainstem. Subcortical fMRI must overcome two challenges: spatial resolution and physiological noise. Here we describe an optimized set of techniques developed to perform high-resolution fMRI in human SC, a structure on the dorsal surface of the midbrain; the methods can also be used to image other brainstem and subcortical structures.
High-resolution (1.2 mm voxels) fMRI of the SC requires a non-conventional approach. The desired spatial sampling is obtained using a multi-shot (interleaved) spiral acquisition1. Since, T2* of SC tissue is longer than in cortex, a correspondingly longer echo time (TE ~ 40 msec) is used to maximize functional contrast. To cover the full extent of the SC, 8-10 slices are obtained. For each session a structural anatomy with the same slice prescription as the fMRI is also obtained, which is used to align the functional data to a high-resolution reference volume.
In a separate session, for each subject, we create a high-resolution (0.7 mm sampling) reference volume using a T1-weighted sequence that gives good tissue contrast. In the reference volume, the midbrain region is segmented using the ITK-SNAP software application2. This segmentation is used to create a 3D surface representation of the midbrain that is both smooth and accurate3. The surface vertices and normals are used to create a map of depth from the midbrain surface within the tissue4.
Functional data is transformed into the coordinate system of the segmented reference volume. Depth associations of the voxels enable the averaging of fMRI time series data within specified depth ranges to improve signal quality. Data is rendered on the 3D surface for visualization.
In our lab we use this technique for measuring topographic maps of visual stimulation and covert and overt visual attention within the SC1. As an example, we demonstrate the topographic representation of polar angle to visual stimulation in SC.

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High-resolution Functional Magnetic Resonance Imaging Methods for Human Midbrain

This article describes techniques to perform high-resolution functional magnetic resonance imaging with 1.2 mm sampling in human midbrain and subcortical structures using a 3T scanner. Use of these techniques to resolve topographic maps of visual stimulation in the human superior colliculus (SC) is given as an example.

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon ...

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12.7K Views.  The University of Texas at Austin. This article describes techniques to perform high-resolution functional magnetic resonance imaging with 1.2 mm sampling in human midbrain and subcortical structures using a 3T scanner. Use of these techniques to resolve topographic maps of visual stimulation in the human superior colliculus (SC) is given as an example.