Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus
Identifieur interne : 000998 ( Pmc/Corpus ); précédent : 000997; suivant : 000999Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus
Auteurs : Abbas F. Sadikot ; M. Mallar Chakravarty ; Gilles Bertrand ; Vladimir V. Rymar ; Fahd Al-Subaie ; D. Louis CollinsSource :
- Frontiers in Systems Neuroscience [ 1662-5137 ] ; 2011.
Abstract
Functional brain imaging and neurosurgery in subcortical areas often requires visualization of brain nuclei beyond the resolution of current magnetic resonance imaging (MRI) methods. We present techniques used to create: (1) a lower resolution 3D atlas, based on the Schaltenbrand and Wahren print atlas, which was integrated into a stereotactic neurosurgery planning and visualization platform (VIPER); and (2) a higher resolution 3D atlas derived from a single set of manually segmented histological slices containing nuclei of the basal ganglia, thalamus, basal forebrain, and medial temporal lobe. Both atlases were integrated to a canonical MRI (Colin27) from a young male participant by manually identifying homologous landmarks. The lower resolution atlas was then warped to fit the MRI based on the identified landmarks. A pseudo-MRI representation of the high-resolution atlas was created, and a non-linear transformation was calculated in order to match the atlas to the template MRI. The atlas can then be warped to match the anatomy of Parkinson's disease surgical candidates by using 3D automated non-linear deformation methods. By way of functional validation of the atlas, the location of the sensory thalamus was correlated with stereotactic intraoperative physiological data. The position of subthalamic electrode positions in patients with Parkinson's disease was also evaluated in the atlas-integrated MRI space. Finally, probabilistic maps of subthalamic stimulation electrodes were developed, in order to allow group analysis of the location of contacts associated with the best motor outcomes. We have therefore developed, and are continuing to validate, a high-resolution computerized MRI-integrated 3D histological atlas, which is useful in functional neurosurgery, and for functional and anatomical studies of the human basal ganglia, thalamus, and basal forebrain.
Url:
DOI: 10.3389/fnsys.2011.00071
PubMed: 21922002
PubMed Central: 3167101
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus</title><author><name sortKey="Sadikot, Abbas F" sort="Sadikot, Abbas F" uniqKey="Sadikot A" first="Abbas F." last="Sadikot">Abbas F. Sadikot</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Chakravarty, M Mallar" sort="Chakravarty, M Mallar" uniqKey="Chakravarty M" first="M. Mallar" last="Chakravarty">M. Mallar Chakravarty</name><affiliation><nlm:aff id="aff2"><institution>The McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Bertrand, Gilles" sort="Bertrand, Gilles" uniqKey="Bertrand G" first="Gilles" last="Bertrand">Gilles Bertrand</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Rymar, Vladimir V" sort="Rymar, Vladimir V" uniqKey="Rymar V" first="Vladimir V." last="Rymar">Vladimir V. Rymar</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Al Subaie, Fahd" sort="Al Subaie, Fahd" uniqKey="Al Subaie F" first="Fahd" last="Al-Subaie">Fahd Al-Subaie</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Collins, D Louis" sort="Collins, D Louis" uniqKey="Collins D" first="D. Louis" last="Collins">D. Louis Collins</name><affiliation><nlm:aff id="aff2"><institution>The McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21922002</idno><idno type="pmc">3167101</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167101</idno><idno type="RBID">PMC:3167101</idno><idno type="doi">10.3389/fnsys.2011.00071</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000998</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000998</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus</title><author><name sortKey="Sadikot, Abbas F" sort="Sadikot, Abbas F" uniqKey="Sadikot A" first="Abbas F." last="Sadikot">Abbas F. Sadikot</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Chakravarty, M Mallar" sort="Chakravarty, M Mallar" uniqKey="Chakravarty M" first="M. Mallar" last="Chakravarty">M. Mallar Chakravarty</name><affiliation><nlm:aff id="aff2"><institution>The McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Bertrand, Gilles" sort="Bertrand, Gilles" uniqKey="Bertrand G" first="Gilles" last="Bertrand">Gilles Bertrand</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Rymar, Vladimir V" sort="Rymar, Vladimir V" uniqKey="Rymar V" first="Vladimir V." last="Rymar">Vladimir V. Rymar</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Al Subaie, Fahd" sort="Al Subaie, Fahd" uniqKey="Al Subaie F" first="Fahd" last="Al-Subaie">Fahd Al-Subaie</name><affiliation><nlm:aff id="aff1"><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author><author><name sortKey="Collins, D Louis" sort="Collins, D Louis" uniqKey="Collins D" first="D. Louis" last="Collins">D. Louis Collins</name><affiliation><nlm:aff id="aff2"><institution>The McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></nlm:aff></affiliation></author></analytic><series><title level="j">Frontiers in Systems Neuroscience</title><idno type="eISSN">1662-5137</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Functional brain imaging and neurosurgery in subcortical areas often requires visualization of brain nuclei beyond the resolution of current magnetic resonance imaging (MRI) methods. We present techniques used to create: (1) a lower resolution 3D atlas, based on the Schaltenbrand and Wahren print atlas, which was integrated into a stereotactic neurosurgery planning and visualization platform (VIPER); and (2) a higher resolution 3D atlas derived from a single set of manually segmented histological slices containing nuclei of the basal ganglia, thalamus, basal forebrain, and medial temporal lobe. Both atlases were integrated to a canonical MRI (Colin27) from a young male participant by manually identifying homologous landmarks. The lower resolution atlas was then warped to fit the MRI based on the identified landmarks. A pseudo-MRI representation of the high-resolution atlas was created, and a non-linear transformation was calculated in order to match the atlas to the template MRI. The atlas can then be warped to match the anatomy of Parkinson's disease surgical candidates by using 3D automated non-linear deformation methods. By way of functional validation of the atlas, the location of the sensory thalamus was correlated with stereotactic intraoperative physiological data. The position of subthalamic electrode positions in patients with Parkinson's disease was also evaluated in the atlas-integrated MRI space. Finally, probabilistic maps of subthalamic stimulation electrodes were developed, in order to allow group analysis of the location of contacts associated with the best motor outcomes. We have therefore developed, and are continuing to validate, a high-resolution computerized MRI-integrated 3D histological atlas, which is useful in functional neurosurgery, and for functional and anatomical studies of the human basal ganglia, thalamus, and basal forebrain.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Afshar, F" uniqKey="Afshar F">F. Afshar</name></author><author><name sortKey="Watkins, E S" uniqKey="Watkins E">E. S. Watkins</name></author><author><name sortKey="Yap, J C" uniqKey="Yap J">J. C. Yap</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Andrew, J" uniqKey="Andrew J">J. Andrew</name></author><author><name sortKey="Tomlinson, J D W" uniqKey="Tomlinson J">J. D. W. Tomlinson</name></author><author><name sortKey="Watkins, E S" uniqKey="Watkins E">E. S. Watkins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Atkinson, J D" uniqKey="Atkinson J">J. D. Atkinson</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Peters, T M" uniqKey="Peters T">T. M. Peters</name></author><author><name sortKey="Pike, G B" uniqKey="Pike G">G. B. Pike</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bardinet, E" uniqKey="Bardinet E">E. Bardinet</name></author><author><name sortKey="Bhattacharjee, M" uniqKey="Bhattacharjee M">M. Bhattacharjee</name></author><author><name sortKey="Dormont, D" uniqKey="Dormont D">D. Dormont</name></author><author><name sortKey="Pidoux, B" uniqKey="Pidoux B">B. Pidoux</name></author><author><name sortKey="Malandain, G" uniqKey="Malandain G">G. Malandain</name></author><author><name sortKey="Schupbach, M" uniqKey="Schupbach M">M. Schupbach</name></author><author><name sortKey="Ayache, N" uniqKey="Ayache N">N. Ayache</name></author><author><name sortKey="Cornu, P" uniqKey="Cornu P">P. Cornu</name></author><author><name sortKey="Agid, Y" uniqKey="Agid Y">Y. Agid</name></author><author><name sortKey="Yelnik, J" uniqKey="Yelnik J">J. Yelnik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berks, G" uniqKey="Berks G">G. Berks</name></author><author><name sortKey="Pohl, G" uniqKey="Pohl G">G. Pohl</name></author><author><name sortKey="Keyserlingk, D G" uniqKey="Keyserlingk D">D. G. Keyserlingk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Oliver, A" uniqKey="Oliver A">A. Oliver</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bhattacharjee, M" uniqKey="Bhattacharjee M">M. Bhattacharjee</name></author><author><name sortKey="Pitiot, A" uniqKey="Pitiot A">A. Pitiot</name></author><author><name sortKey="Roche, A" uniqKey="Roche A">A. Roche</name></author><author><name sortKey="Dormont, D" uniqKey="Dormont D">D. Dormont</name></author><author><name sortKey="Bardinet, E" uniqKey="Bardinet E">E. Bardinet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bookstein, F L" uniqKey="Bookstein F">F. L. Bookstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakravarty, M M" uniqKey="Chakravarty M">M. M. Chakravarty</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Hodge, C P" uniqKey="Hodge C">C. P. Hodge</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakravarty, M M" uniqKey="Chakravarty M">M. M. Chakravarty</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Mongia, S" uniqKey="Mongia S">S. Mongia</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakravarty, M M" uniqKey="Chakravarty M">M. M. Chakravarty</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Germann, J" uniqKey="Germann J">J. Germann</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakravarty, M M" uniqKey="Chakravarty M">M. M. Chakravarty</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Germann, J" uniqKey="Germann J">J. Germann</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chakravarty, M M" uniqKey="Chakravarty M">M. M. Chakravarty</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Germann, J" uniqKey="Germann J">J. Germann</name></author><author><name sortKey="Hellier, P" uniqKey="Hellier P">P. Hellier</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cline, H E" uniqKey="Cline H">H. E. Cline</name></author><author><name sortKey="Dumoulin, C L" uniqKey="Dumoulin C">C. L. Dumoulin</name></author><author><name sortKey="Hart, H R" uniqKey="Hart H">H. R. Hart</name></author><author><name sortKey="Lorensen, W E" uniqKey="Lorensen W">W. E. Lorensen</name></author><author><name sortKey="Ludke, S" uniqKey="Ludke S">S. Ludke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author><author><name sortKey="Evans, A C" uniqKey="Evans A">A. C. Evans</name></author><author><name sortKey="Holmes, C" uniqKey="Holmes C">C. Holmes</name></author><author><name sortKey="Peters, T M" uniqKey="Peters T">T. M. Peters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="D Haese, P F" uniqKey="D Haese P">P. F. D'Haese</name></author><author><name sortKey="Cetinkaya, E" uniqKey="Cetinkaya E">E. Cetinkaya</name></author><author><name sortKey="Konrad, P E" uniqKey="Konrad P">P. E. Konrad</name></author><author><name sortKey="Kao, C" uniqKey="Kao C">C. Kao</name></author><author><name sortKey="Dawant, B M" uniqKey="Dawant B">B. M. Dawant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Duerden, E G" uniqKey="Duerden E">E. G. Duerden</name></author><author><name sortKey="Finnis, K W" uniqKey="Finnis K">K. W. Finnis</name></author><author><name sortKey="Peters, T M" uniqKey="Peters T">T. M. Peters</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Duval, C" uniqKey="Duval C">C. Duval</name></author><author><name sortKey="Panisset, M" uniqKey="Panisset M">M. Panisset</name></author><author><name sortKey="Strafella, A P" uniqKey="Strafella A">A. P. Strafella</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gloor, P" uniqKey="Gloor P">P. Gloor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Bertrand, G" uniqKey="Bertrand G">G. Bertrand</name></author><author><name sortKey="Thompson, C J" uniqKey="Thompson C">C. J. Thompson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hardy, T L" uniqKey="Hardy T">T. L. Hardy</name></author><author><name sortKey="Smith, J R" uniqKey="Smith J">J. R. Smith</name></author><author><name sortKey="Brynildson, L R" uniqKey="Brynildson L">L. R. Brynildson</name></author><author><name sortKey="Flanigan, H F" uniqKey="Flanigan H">H. F. Flanigan</name></author><author><name sortKey="Gray, J G" uniqKey="Gray J">J. G. Gray</name></author><author><name sortKey="Spurlock, D" uniqKey="Spurlock D">D. Spurlock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hassler, R" uniqKey="Hassler R">R. Hassler</name></author><author><name sortKey="Mundinger, F" uniqKey="Mundinger F">F. Mundinger</name></author><author><name sortKey="Riechert, T" uniqKey="Riechert T">T. Riechert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heimer, L" uniqKey="Heimer L">L. Heimer</name></author><author><name sortKey="Harlan, R E" uniqKey="Harlan R">R. E. Harlan</name></author><author><name sortKey="Alheid, G F" uniqKey="Alheid G">G. F. Alheid</name></author><author><name sortKey="Garcia, M M" uniqKey="Garcia M">M. M. Garcia</name></author><author><name sortKey="De Olmos, J" uniqKey="De Olmos J">J. de Olmos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hellier, P" uniqKey="Hellier P">P. Hellier</name></author><author><name sortKey="Barillot, C" uniqKey="Barillot C">C. Barillot</name></author><author><name sortKey="Corouge, I" uniqKey="Corouge I">I. Corouge</name></author><author><name sortKey="Gibaud, B" uniqKey="Gibaud B">B. Gibaud</name></author><author><name sortKey="Le Goualher, G" uniqKey="Le Goualher G">G. Le Goualher</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author><author><name sortKey="Evans, A" uniqKey="Evans A">A. Evans</name></author><author><name sortKey="Malandain, G" uniqKey="Malandain G">G. Malandain</name></author><author><name sortKey="Ayache, N" uniqKey="Ayache N">N. Ayache</name></author><author><name sortKey="Christensen, G E" uniqKey="Christensen G">G. E. Christensen</name></author><author><name sortKey="Johnson, H J" uniqKey="Johnson H">H. J. Johnson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirai, T" uniqKey="Hirai T">T. Hirai</name></author><author><name sortKey="Jones, E G" uniqKey="Jones E">E. G. Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirai, T" uniqKey="Hirai T">T. Hirai</name></author><author><name sortKey="Jones, E G" uniqKey="Jones E">E. G. Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Holmes, C J" uniqKey="Holmes C">C. J. Holmes</name></author><author><name sortKey="Hoge, R" uniqKey="Hoge R">R. Hoge</name></author><author><name sortKey="Collins, L" uniqKey="Collins L">L. Collins</name></author><author><name sortKey="Woods, R" uniqKey="Woods R">R. Woods</name></author><author><name sortKey="Toga, A W" uniqKey="Toga A">A. W. Toga</name></author><author><name sortKey="Evans, A C" uniqKey="Evans A">A. C. Evans</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jones, E G" uniqKey="Jones E">E. G. Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kazarnovskaya, M I" uniqKey="Kazarnovskaya M">M. I. Kazarnovskaya</name></author><author><name sortKey="Borodkin, S M" uniqKey="Borodkin S">S. M. Borodkin</name></author><author><name sortKey="Shabalov, V A" uniqKey="Shabalov V">V. A. Shabalov</name></author><author><name sortKey="Krivosheina, V Y" uniqKey="Krivosheina V">V. Y. Krivosheina</name></author><author><name sortKey="Golanov, A V" uniqKey="Golanov A">A. V. Golanov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klein, A" uniqKey="Klein A">A. Klein</name></author><author><name sortKey="Andersson, J" uniqKey="Andersson J">J. Andersson</name></author><author><name sortKey="Ardekani, B A" uniqKey="Ardekani B">B. A. Ardekani</name></author><author><name sortKey="Ashburner, J" uniqKey="Ashburner J">J. Ashburner</name></author><author><name sortKey="Avants, B" uniqKey="Avants B">B. Avants</name></author><author><name sortKey="Chiang, M C" uniqKey="Chiang M">M. C. Chiang</name></author><author><name sortKey="Christensen, G E" uniqKey="Christensen G">G. E. Christensen</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author><author><name sortKey="Gee, J" uniqKey="Gee J">J. Gee</name></author><author><name sortKey="Hellier, P" uniqKey="Hellier P">P. Hellier</name></author><author><name sortKey="Song, J H" uniqKey="Song J">J. H. Song</name></author><author><name sortKey="Jenkinson, M" uniqKey="Jenkinson M">M. Jenkinson</name></author><author><name sortKey="Lepage, C" uniqKey="Lepage C">C. Lepage</name></author><author><name sortKey="Rueckert, D" uniqKey="Rueckert D">D. Rueckert</name></author><author><name sortKey="Thompson, P" uniqKey="Thompson P">P. Thompson</name></author><author><name sortKey="Vercauteren, T" uniqKey="Vercauteren T">T. Vercauteren</name></author><author><name sortKey="Woods, R P" uniqKey="Woods R">R. P. Woods</name></author><author><name sortKey="Mann, J J" uniqKey="Mann J">J. J. Mann</name></author><author><name sortKey="Parsey, R V" uniqKey="Parsey R">R. V. Parsey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krauth, A" uniqKey="Krauth A">A. Krauth</name></author><author><name sortKey="Blanc, R" uniqKey="Blanc R">R. Blanc</name></author><author><name sortKey="Poveda, A" uniqKey="Poveda A">A. Poveda</name></author><author><name sortKey="Jeanmonod, D" uniqKey="Jeanmonod D">D. Jeanmonod</name></author><author><name sortKey="Morel, A" uniqKey="Morel A">A. Morel</name></author><author><name sortKey="Szekely, G" uniqKey="Szekely G">G. Szekely</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Macdonald, D" uniqKey="Macdonald D">D. Macdonald</name></author><author><name sortKey="Avis, D" uniqKey="Avis D">D. Avis</name></author><author><name sortKey="Evans, A C" uniqKey="Evans A">A. C. Evans</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mai, J K" uniqKey="Mai J">J. K. Mai</name></author><author><name sortKey="Assheuer, J" uniqKey="Assheuer J">J. Assheuer</name></author><author><name sortKey="Paxinos, G" uniqKey="Paxinos G">G. Paxinos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mai, J K" uniqKey="Mai J">J. K. Mai</name></author><author><name sortKey="Voss, T" uniqKey="Voss T">T. Voss</name></author><author><name sortKey="Paxinos, G" uniqKey="Paxinos G">G. Paxinos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Malandain, G" uniqKey="Malandain G">G. Malandain</name></author><author><name sortKey="Bardinet, E" uniqKey="Bardinet E">E. Bardinet</name></author><author><name sortKey="Nelissen, K" uniqKey="Nelissen K">K. Nelissen</name></author><author><name sortKey="Vanduffel, W" uniqKey="Vanduffel W">W. Vanduffel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morel, A" uniqKey="Morel A">A. Morel</name></author><author><name sortKey="Magnin, M" uniqKey="Magnin M">M. Magnin</name></author><author><name sortKey="Jeanmonod, D" uniqKey="Jeanmonod D">D. Jeanmonod</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Niemann, K" uniqKey="Niemann K">K. Niemann</name></author><author><name sortKey="Naujokat, C" uniqKey="Naujokat C">C. Naujokat</name></author><author><name sortKey="Pohl, G" uniqKey="Pohl G">G. Pohl</name></author><author><name sortKey="Wollner, C" uniqKey="Wollner C">C. Wollner</name></author><author><name sortKey="Von Keyserlingk, D" uniqKey="Von Keyserlingk D">D. von Keyserlingk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Niemann, K" uniqKey="Niemann K">K. Niemann</name></author><author><name sortKey="Van Nieuwenhofen, I" uniqKey="Van Nieuwenhofen I">I. van Nieuwenhofen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author><author><name sortKey="Belov, D" uniqKey="Belov D">D. Belov</name></author><author><name sortKey="Thirunavuukarasuu, A" uniqKey="Thirunavuukarasuu A">A. Thirunavuukarasuu</name></author><author><name sortKey="Benabid, A L" uniqKey="Benabid A">A. L. Benabid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author><author><name sortKey="Fang, A" uniqKey="Fang A">A. Fang</name></author><author><name sortKey="Nguyen, B T" uniqKey="Nguyen B">B. T. Nguyen</name></author><author><name sortKey="Raphel, J K" uniqKey="Raphel J">J. K. Raphel</name></author><author><name sortKey="Jagannathan, L" uniqKey="Jagannathan L">L. Jagannathan</name></author><author><name sortKey="Raghavan, R" uniqKey="Raghavan R">R. Raghavan</name></author><author><name sortKey="Bryan, R N" uniqKey="Bryan R">R. N. Bryan</name></author><author><name sortKey="Miller, G A" uniqKey="Miller G">G. A. Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J. Liu</name></author><author><name sortKey="Thirunavuukarasuu, A" uniqKey="Thirunavuukarasuu A">A. Thirunavuukarasuu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author><author><name sortKey="Thirunavuukarasuu, A" uniqKey="Thirunavuukarasuu A">A. Thirunavuukarasuu</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J. Liu</name></author><author><name sortKey="Benabid, A L" uniqKey="Benabid A">A. L. Benabid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olszewski, J" uniqKey="Olszewski J">J. Olszewski</name></author><author><name sortKey="Baxter, D W" uniqKey="Baxter D">D. W. Baxter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pallavaram, S" uniqKey="Pallavaram S">S. Pallavaram</name></author><author><name sortKey="Dawant, B M" uniqKey="Dawant B">B. M. Dawant</name></author><author><name sortKey="Remple, M S" uniqKey="Remple M">M. S. Remple</name></author><author><name sortKey="Neimat, J S" uniqKey="Neimat J">J. S. Neimat</name></author><author><name sortKey="Kao, C" uniqKey="Kao C">C. Kao</name></author><author><name sortKey="Konrad, P E" uniqKey="Konrad P">P. E. Konrad</name></author><author><name sortKey="D Haese, P F" uniqKey="D Haese P">P. F. D'Haese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robbins, S" uniqKey="Robbins S">S. Robbins</name></author><author><name sortKey="Evans, A C" uniqKey="Evans A">A. C. Evans</name></author><author><name sortKey="Collins, D L" uniqKey="Collins D">D. L. Collins</name></author><author><name sortKey="Whitesides, S" uniqKey="Whitesides S">S. Whitesides</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sadikot, A" uniqKey="Sadikot A">A. Sadikot</name></author><author><name sortKey="Mongia, S" uniqKey="Mongia S">S. Mongia</name></author><author><name sortKey="Chakravarty, M" uniqKey="Chakravarty M">M. Chakravarty</name></author><author><name sortKey="Panisset, M" uniqKey="Panisset M">M. Panisset</name></author><author><name sortKey="Collins, D" uniqKey="Collins D">D. Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sather, M D" uniqKey="Sather M">M. D. Sather</name></author><author><name sortKey="Patil, A A" uniqKey="Patil A">A. A. Patil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schaltenbrand, G" uniqKey="Schaltenbrand G">G. Schaltenbrand</name></author><author><name sortKey="Bailey, P" uniqKey="Bailey P">P. Bailey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schaltenbrand, G" uniqKey="Schaltenbrand G">G. Schaltenbrand</name></author><author><name sortKey="Wahren, W" uniqKey="Wahren W">W. Wahren</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sramka, M" uniqKey="Sramka M">M. Sramka</name></author><author><name sortKey="Ruzicky, E" uniqKey="Ruzicky E">E. Ruzicky</name></author><author><name sortKey="Novotny, M" uniqKey="Novotny M">M. Novotny</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="St Jean, P" uniqKey="St Jean P">P. St-Jean</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Collins, L" uniqKey="Collins L">L. Collins</name></author><author><name sortKey="Clonda, D" uniqKey="Clonda D">D. Clonda</name></author><author><name sortKey="Kasrai, R" uniqKey="Kasrai R">R. Kasrai</name></author><author><name sortKey="Evans, A C" uniqKey="Evans A">A. C. Evans</name></author><author><name sortKey="Peters, T M" uniqKey="Peters T">T. M. Peters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strafella, A P" uniqKey="Strafella A">A. P. Strafella</name></author><author><name sortKey="Vanderwerf, Y" uniqKey="Vanderwerf Y">Y. Vanderwerf</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Talairach, J" uniqKey="Talairach J">J. Talairach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Talairach, J" uniqKey="Talairach J">J. Talairach</name></author><author><name sortKey="Tournoux, P" uniqKey="Tournoux P">P. Tournoux</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tyvaert, L" uniqKey="Tyvaert L">L. Tyvaert</name></author><author><name sortKey="Chassagnon, S" uniqKey="Chassagnon S">S. Chassagnon</name></author><author><name sortKey="Sadikot, A" uniqKey="Sadikot A">A. Sadikot</name></author><author><name sortKey="Levan, P" uniqKey="Levan P">P. Levan</name></author><author><name sortKey="Dubeau, F" uniqKey="Dubeau F">F. Dubeau</name></author><author><name sortKey="Gotman, J" uniqKey="Gotman J">J. Gotman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Buren, J M" uniqKey="Van Buren J">J. M. Van Buren</name></author><author><name sortKey="Borke, R C" uniqKey="Borke R">R. C. Borke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Buren, J M" uniqKey="Van Buren J">J. M. Van Buren</name></author><author><name sortKey="Maccubbin, D A" uniqKey="Maccubbin D">D. A. Maccubbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Der Werf, Y D" uniqKey="Van Der Werf Y">Y. D. Van Der Werf</name></author><author><name sortKey="Sadikot, A F" uniqKey="Sadikot A">A. F. Sadikot</name></author><author><name sortKey="Strafella, A P" uniqKey="Strafella A">A. P. Strafella</name></author><author><name sortKey="Paus, T" uniqKey="Paus T">T. Paus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Walker, A E" uniqKey="Walker A">A. E. Walker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yelnik, J" uniqKey="Yelnik J">J. Yelnik</name></author><author><name sortKey="Bardinet, E" uniqKey="Bardinet E">E. Bardinet</name></author><author><name sortKey="Dormont, D" uniqKey="Dormont D">D. Dormont</name></author><author><name sortKey="Malandain, G" uniqKey="Malandain G">G. Malandain</name></author><author><name sortKey="Ourselin, S" uniqKey="Ourselin S">S. Ourselin</name></author><author><name sortKey="Tande, D" uniqKey="Tande D">D. Tande</name></author><author><name sortKey="Karachi, C" uniqKey="Karachi C">C. Karachi</name></author><author><name sortKey="Ayache, N" uniqKey="Ayache N">N. Ayache</name></author><author><name sortKey="Cornu, P" uniqKey="Cornu P">P. Cornu</name></author><author><name sortKey="Agid, Y" uniqKey="Agid Y">Y. Agid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yelnik, J" uniqKey="Yelnik J">J. Yelnik</name></author><author><name sortKey="Damier, P" uniqKey="Damier P">P. Damier</name></author><author><name sortKey="Bejjani, B P" uniqKey="Bejjani B">B. P. Bejjani</name></author><author><name sortKey="Francois, C" uniqKey="Francois C">C. Francois</name></author><author><name sortKey="Gervais, D" uniqKey="Gervais D">D. Gervais</name></author><author><name sortKey="Dormont, D" uniqKey="Dormont D">D. Dormont</name></author><author><name sortKey="Arnulf, I" uniqKey="Arnulf I">I. Arnulf</name></author><author><name sortKey="Bonnet, M A" uniqKey="Bonnet M">M. A. Bonnet</name></author><author><name sortKey="Cornu, P" uniqKey="Cornu P">P. Cornu</name></author><author><name sortKey="Pidoux, B" uniqKey="Pidoux B">B. Pidoux</name></author><author><name sortKey="Agid, Y" uniqKey="Agid Y">Y. Agid</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yeo, T T" uniqKey="Yeo T">T. T. Yeo</name></author><author><name sortKey="Nowinski, W L" uniqKey="Nowinski W">W. L. Nowinski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yoshida, M" uniqKey="Yoshida M">M. Yoshida</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Syst Neurosci</journal-id><journal-id journal-id-type="publisher-id">Front. Syst. Neurosci.</journal-id><journal-title-group><journal-title>Frontiers in Systems Neuroscience</journal-title></journal-title-group><issn pub-type="epub">1662-5137</issn><publisher><publisher-name>Frontiers Research Foundation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21922002</article-id><article-id pub-id-type="pmc">3167101</article-id><article-id pub-id-type="doi">10.3389/fnsys.2011.00071</article-id><article-categories><subj-group subj-group-type="heading"><subject>Neuroscience</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sadikot</surname><given-names>Abbas F.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001">*</xref></contrib><contrib contrib-type="author"><name><surname>Chakravarty</surname><given-names>M. Mallar</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bertrand</surname><given-names>Gilles</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rymar</surname><given-names>Vladimir V.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Al-Subaie</surname><given-names>Fahd</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Collins</surname><given-names>D. Louis</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Cone Laboratory for Research in Neurosurgery, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></aff><aff id="aff2"><sup>2</sup><institution>The McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University</institution><country>Montreal, QC, Canada</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: James M. Tepper, Rutgers, The State University of New Jersey, USA</p></fn><fn fn-type="edited-by"><p>Reviewed by: Christine E. Collins, Vanderbilt University, USA; Yoland Smith, Emory University, USA</p></fn><corresp id="fn001">*Correspondence: Abbas F. Sadikot, Cone Laboratory, Montreal Neurological Institute, 3801 University Street, Montreal, QC, Canada H3A2B4. e-mail: <email>abbas.sadikot@mcgill.ca</email></corresp></author-notes><pub-date pub-type="epreprint"><day>05</day><month>6</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>06</day><month>9</month><year>2011</year></pub-date><pub-date pub-type="collection"><year>2011</year></pub-date><volume>5</volume><elocation-id>71</elocation-id><history><date date-type="received"><day>13</day><month>5</month><year>2011</year></date><date date-type="accepted"><day>08</day><month>8</month><year>2011</year></date></history><permissions><copyright-statement>Copyright © 2011 Sadikot, Chakravarty, Bertrand, Rymar, Al-Subaie and Collins.</copyright-statement><copyright-year>2011</copyright-year><license license-type="open-access" xlink:href="http://www.frontiersin.org/licenseagreement"><license-p>This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.</license-p></license></permissions><abstract><p>Functional brain imaging and neurosurgery in subcortical areas often requires visualization of brain nuclei beyond the resolution of current magnetic resonance imaging (MRI) methods. We present techniques used to create: (1) a lower resolution 3D atlas, based on the Schaltenbrand and Wahren print atlas, which was integrated into a stereotactic neurosurgery planning and visualization platform (VIPER); and (2) a higher resolution 3D atlas derived from a single set of manually segmented histological slices containing nuclei of the basal ganglia, thalamus, basal forebrain, and medial temporal lobe. Both atlases were integrated to a canonical MRI (Colin27) from a young male participant by manually identifying homologous landmarks. The lower resolution atlas was then warped to fit the MRI based on the identified landmarks. A pseudo-MRI representation of the high-resolution atlas was created, and a non-linear transformation was calculated in order to match the atlas to the template MRI. The atlas can then be warped to match the anatomy of Parkinson's disease surgical candidates by using 3D automated non-linear deformation methods. By way of functional validation of the atlas, the location of the sensory thalamus was correlated with stereotactic intraoperative physiological data. The position of subthalamic electrode positions in patients with Parkinson's disease was also evaluated in the atlas-integrated MRI space. Finally, probabilistic maps of subthalamic stimulation electrodes were developed, in order to allow group analysis of the location of contacts associated with the best motor outcomes. We have therefore developed, and are continuing to validate, a high-resolution computerized MRI-integrated 3D histological atlas, which is useful in functional neurosurgery, and for functional and anatomical studies of the human basal ganglia, thalamus, and basal forebrain.</p></abstract><kwd-group><kwd>brain atlas</kwd><kwd>Parkinson's disease</kwd><kwd>stereotactic neurosurgery</kwd><kwd>image guidance</kwd></kwd-group><counts><fig-count count="4"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="69"></ref-count><page-count count="8"></page-count><word-count count="6689"></word-count></counts></article-meta></front><body><sec sec-type="introduction"><title>Introduction</title><p>Despite impressive gains in medical imaging during the last two decades, significant challenges remain when visualizing the structure of the living brain. The resolution and contrast of standard <italic>in vivo</italic> magnetic resonance imaging (MRI) is well below that required to visualize subnuclei and fiber tracts of the basal ganglia, thalamus, and brainstem. Since image-guided neurosurgery for Parkinson's disease often targets subnuclei of the thalamus, subthalamic area, basal ganglia, and brainstem, reliable targeting needs to be supplemented with invasive neurophysiological methods. Furthermore, advances in functional brain imaging have allowed increasing visualization of activation in subcortical brain areas, but only low-resolution atlases are available for interpretation of these changes. Most available print atlases of the human brain delineate subcortical nuclei in tissue sectioned in three planes, derived from different hemispheres using multiple brains (Olszewski and Baxter, <xref ref-type="bibr" rid="B49">1954</xref>; Talairach, <xref ref-type="bibr" rid="B59">1957</xref>; Schaltenbrand and Bailey, <xref ref-type="bibr" rid="B54">1959</xref>; Van Buren and Maccubbin, <xref ref-type="bibr" rid="B63">1962</xref>; Andrew et al., <xref ref-type="bibr" rid="B2">1969</xref>; Van Buren and Borke, <xref ref-type="bibr" rid="B62">1972</xref>; Schaltenbrand and Wahren, <xref ref-type="bibr" rid="B55">1977</xref>; Afshar et al., <xref ref-type="bibr" rid="B1">1978</xref>; Talairach and Tournoux, <xref ref-type="bibr" rid="B60">1988</xref>). Bertrand and Thompson published the first computerized digitized atlas, which was derived from the Schaltenbrand print atlas. This atlas could be mapped to stereotactic ventriculograms using constrained affine transformations (Bertrand et al., <xref ref-type="bibr" rid="B6">1973</xref>). The atlas was used in stereotactic neurosurgery of the thalamus and basal ganglia, and also served as the basis for functional atlases of deep brain stimulation responses (Hardy et al., <xref ref-type="bibr" rid="B20">1979a</xref>,<xref ref-type="bibr" rid="B21">b</xref>,<xref ref-type="bibr" rid="B22">c</xref>, <xref ref-type="bibr" rid="B25">1981</xref>). A variety of digital atlases have since been created from original print versions (Yoshida, <xref ref-type="bibr" rid="B69">1987</xref>; Kazarnovskaya et al., <xref ref-type="bibr" rid="B34">1991</xref>; Hardy et al., <xref ref-type="bibr" rid="B26">1992</xref>; Niemann et al., <xref ref-type="bibr" rid="B42">1994</xref>; Nowinski et al., <xref ref-type="bibr" rid="B46">1997</xref>; Sramka et al., <xref ref-type="bibr" rid="B56">1997</xref>; Yeo and Nowinski, <xref ref-type="bibr" rid="B68">1997</xref>; Niemann and van Nieuwenhofen, <xref ref-type="bibr" rid="B43">1999</xref>; Yelnik et al., <xref ref-type="bibr" rid="B67">2000</xref>; Berks et al., <xref ref-type="bibr" rid="B5">2001</xref>).</p><p>Challenges faced when creating computerized 3D digital atlases from print atlases include: (1) Print atlases often have low inter-slice resolution and variable inter-slice distances. Reconstructed nuclei data may be fractured, reducing atlas utility. Furthermore, minor errors in photographic representations in stereotactic space can result in a shift between reconstructed slices, making image integration difficult in 3D space. Robust reconstruction algorithms that account for slice-to-slice variability, and anatomical differences between the atlas and patient data, can help enhance the quality of 3D visualization and atlas integration (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>, <xref ref-type="bibr" rid="B12">2008</xref>). (2) Differences in stereotaxic location of nuclear structures may be noted when comparing data derived in different planes from different hemispheres. Simple representation of the three planes of a print atlas is therefore not useful in computerized atlas aided analysis of neurosurgical plans, since the data sets do not match in all planes. (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Niemann and van Nieuwenhofen, <xref ref-type="bibr" rid="B43">1999</xref>; Nowinski et al., <xref ref-type="bibr" rid="B45">2005</xref>, <xref ref-type="bibr" rid="B47">2008</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>,<xref ref-type="bibr" rid="B10">b</xref>, <xref ref-type="bibr" rid="B12">2008</xref>, <xref ref-type="bibr" rid="B13">2009</xref>; Sather and Patil, <xref ref-type="bibr" rid="B53">2007</xref>; Yelnik et al., <xref ref-type="bibr" rid="B66">2007</xref>). Multiplanar reconstruction from a unique histological data set is more useful (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>) although only low resolution is obtained in most cases due to lack of detail in the source data. (3) Histological artifacts related to different stains (e.g., myelin, Nissl) can be problematic, especially in large sections, limiting proper identification of outlines of nuclei and tracts. Furthermore, thalamic nuclear nomenclature is highly complex, making it difficult to provide reliable outlines in multiplanar 3D mode on the basis of an initially low-resolution data set. (4) Tissue inhomogeneity can occur due to shear stress on sectioning, and artifacts can result from histological processing and slice mounting, further reducing the ability to interpret the underlying anatomy. For this reason, it is necessary to apply computerized reconstruction methods to minimize slice-to-slice variations in tissue morphology and staining intensity. (5) Classical atlases such as that of Schaltenbrand are based largely on detailed histological delineations using Hassler's nomenclature (Hassler et al., <xref ref-type="bibr" rid="B27">1965</xref>; Schaltenbrand and Wahren, <xref ref-type="bibr" rid="B55">1977</xref>). This terminology, which includes a distinct parcellation of the thalamus, has proved useful for neurosurgeons, and classical anatomists. Correspondence in 3D atlas space of Hassler's terminology with more commonly used thalamic nomenclature based on work in human and non-human primates would be desirable (Hirai and Jones, <xref ref-type="bibr" rid="B31">1989b</xref>).</p><p>Here, we summarize our recent work on the creation and implementation of two digitized 3D atlases of subcortical structures. We first created a lower resolution atlas based on axial slices derived from the Schaltenbrand and Wahren print atlas (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>; Strafella et al., <xref ref-type="bibr" rid="B58">2004</xref>; Duval et al., <xref ref-type="bibr" rid="B18">2006</xref>; Tyvaert et al., <xref ref-type="bibr" rid="B61">2009</xref>). More recently, we created a higher resolution atlas derived from a new set of coronal histological slices, with delineation of thalamic and basal forebrain nuclei based on multiple terminologies (Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>,<xref ref-type="bibr" rid="B10">b</xref>, <xref ref-type="bibr" rid="B13">2009</xref>; Duval et al., <xref ref-type="bibr" rid="B18">2006</xref>). We concurrently developed novel tools for the creation of volumetric voxel-based 3D atlases from histological data sets, and methods for effective integration of the digitized atlases with canonical high-resolution MRI scans, or individual participant or patient MRIs. Availability of high-resolution digitized deformable atlases of subcortical nuclei will greatly aid in image-guided neurosurgery in subcortical areas, and in interpretation of structural and functional brain imaging data.</p></sec><sec sec-type="materials|methods"><title>Materials and Methods</title><p>Two computerized 3D atlases were created. The first atlas was created using the Schaltenbrand and Wahren print atlas. Details of image processing used for atlas development are presented in the Section <xref ref-type="sec" rid="s1">“Results.”</xref> This atlas was integrated into VIPER, a stereotactic visual integration platform for enhanced reality (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>). VIPER allows visualization of stereotactic tools, electrodes, and virtual lesions in the 3D atlas space. The second atlas was created using the postmortem brain of a middle-aged man who died of a non-neurological cause. The brain was fixed in 10% buffered formalin, hemi-sectioned in the mid-sagittal plane, and blocked to obtain the thalamus, basal ganglia, basal forebrain, and temporal lobe of the left hemisphere. The brain was then embedded in paraffin, and sectioned in the coronal plane, perpendicular to the AP–PC plane (Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>). Pairs of 15 μm thick slices were sampled from this data set at 0.70 mm intervals, yielding a total of 86 pairs of slices across the block. For each pair of slices, one was stained with Luxol Fast Blue for myelin, while the other was stained with a Nissl stain for neurons and glia. Subsequent image processing for atlas development is presented in the Section <xref ref-type="sec" rid="s1">“Results.”</xref> Computerized software used for image analysis included Adobe Photoshop 7, and MINC image analysis tools developed at the McConnell Brain Imaging Centre at the MNI (available at: <uri xlink:type="simple" xlink:href="http://www.bic.mni.mcgill.ca/ServicesSoftware">http://www.bic.mni.mcgill.ca/ServicesSoftware</uri>).</p></sec><sec id="s1"><title>Results</title><sec><title>Initial creation of a 3D digitized atlas with a surgical planning platform</title><p>We initially created a digitized computerized 3D version of the atlas of Schaltenbrand and Wahren (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>). The digital atlas was created from an axial data set with varying slice thickness of 0.5–3 mm due to the slice-to-slice distance variations in the original photographic plates (Schaltenbrand and Wahren, <xref ref-type="bibr" rid="B55">1977</xref>). The 2D contour data was extracted into a vector format. Hermite polynomials were applied in order to interpolate the 2D contour data to achieve a 0.5-mm isotropic voxel resolution in the reconstructed 3D data set.</p><p>A methodology was then developed to create a customized version of the Schaltenbrand and Wahren atlas which can be automatically integrated to a patient's MRI scan on a routine basis. The reconstructed 3D digital atlas was first warped to fit Colin27, a widely used high resolution, high signal-to-noise canonical reference MRI volume, which is derived by averaging 27 T1-weighted MRI scans of the same participant (Collins et al., <xref ref-type="bibr" rid="B15">1995</xref>; Holmes et al., <xref ref-type="bibr" rid="B32">1998</xref>). Two hundred fifty homologous point-pairs of landmarks were manually identified on both the digitized atlas and the canonical volume using REGISTER (Macdonald et al., <xref ref-type="bibr" rid="B37">1994</xref>). The volumetric version of the Schaltenbrand atlas was then warped to the reference MRI using Bookstein's 3D thin-plate-spline interpolation approach (Bookstein, <xref ref-type="bibr" rid="B8">1989</xref>). The result of this initial labor-intensive step is a 3D volumetric MRI-integrated reference atlas of the basal ganglia and thalamus.</p><p>The MRI-integrated reference digital atlas may then be integrated to individual patient MRI scans using a non-labor-intensive automated process. An automated non-linear intensity matching algorithm, ANIMAL (Collins et al., <xref ref-type="bibr" rid="B15">1995</xref>), is applied to generate a transform which matches a patient's MRI to the Colin27 MRI average. Application of the inverse of this transformation allows integration of the 3D digital atlas into the patient's MRI reference space. The MRI-integrated atlas can also be used in the VIPER stereotactic platform, which allows visualization of stereotactic targets, neurosurgical instruments (deep brain stimulation leads, leukotomes, retractable searching electrodes), and lesions in the atlas and MRI spaces (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>).</p></sec><sec><title>Development of a higher resolution 3D digitized atlas with incorporation of multiple nomenclatures of nuclei of the thalamus, basal ganglia, and basal forebrain</title><p>While the previously described 3D atlas proved very useful (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>; Strafella et al., <xref ref-type="bibr" rid="B58">2004</xref>; Duval et al., <xref ref-type="bibr" rid="B18">2006</xref>; Van Der Werf et al., <xref ref-type="bibr" rid="B64">2006</xref>; Tyvaert et al., <xref ref-type="bibr" rid="B61">2009</xref>; Duerden et al., <xref ref-type="bibr" rid="B17">2011</xref>) it has limited inherent inter-slice resolution, and contains a limited number of subcortical nuclear structures. Furthermore, the atlas does not present an analysis of homologies between Hassler's terminology and the more recent terminology of Jones and Hirai, based on the so-called “Anglo-American” school and work in non-human primates. In order to help overcome these limitations, we created a new higher resolution atlas with more detailed outlines of subcortical subnuclei, including reference to multiple anatomical nomenclatures (Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>, <xref ref-type="bibr" rid="B13">2009</xref>). The new digital atlas is derived from a single set of high resolution, thin-slice histological data of the basal ganglia, basal forebrain, and thalamus. Consecutive pairs of slices were sampled from this data set at 0.70 mm intervals, and one set was stained with Luxol Fast Blue for myelin, while the other was stained with a Nissl stain for neurons and glia. A total of 86 pairs of slices across the block was analyzed. The atlas contains 105 anatomical structures that were manually delineated by neuroanatomists (GB, AFS, VVR) on the myelin and Nissl stained histological data, using multiple source terminologies for the thalamus, basal ganglia, basal forebrain, and amygdala (Figures <xref ref-type="fig" rid="F1">1</xref>A,B) Within the thalamus, nuclear boundaries were identified according to the terminologies of Hassler (Schaltenbrand and Wahren, <xref ref-type="bibr" rid="B55">1977</xref>), and of Hirai and Jones (Hirai and Jones, <xref ref-type="bibr" rid="B30">1989a</xref>,<xref ref-type="bibr" rid="B31">b</xref>). Detailed work is now continuing in the basal forebrain with further reference to the terminology of Brockhaus, Gloor, Heimer and colleagues, and Paxinos and Mai (Gloor, <xref ref-type="bibr" rid="B19">1997</xref>; Heimer et al., <xref ref-type="bibr" rid="B28">1997</xref>; Mai et al., <xref ref-type="bibr" rid="B39">2008</xref>).</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Outline of nuclei of the human thalamus on a coronal Myelin–Nissl stained section</bold>. The section is taken at the level of the sensory thalamus. Thalamic nuclei are outlined using the terminology in Schaltenbrand's atlas according to Hassler <bold>(A)</bold>, with homologous outlines using the terminology of Hirai and Jones <bold>(B)</bold>.</p></caption><graphic xlink:href="fnsys-05-00071-g001"></graphic></fig><p>The histological data were then reconstructed in 3D using methods described in detail in our previous work (Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>, <xref ref-type="bibr" rid="B12">2008</xref>, <xref ref-type="bibr" rid="B13">2009</xref>). First, an optimized version of the ANIMAL algorithm was developed for slice-to-slice non-linear registration, and was applied throughout the reconstructed data set to minimize morphological misalignment between slices. An intensity correction algorithm was also developed for optimization of the histological data, accounting for staining inhomogeneities, and other processing artifacts, such as tearing, local compression, shearing, or stretching (Malandain et al., <xref ref-type="bibr" rid="B40">2004</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B11">2005</xref>). The correction scheme matches local neighborhoods in each slice using a least-trimmed squares estimator, in order to build a voxel-by-voxel multiplicative field to correct for local variations in image intensities between slices (Chakravarty et al., <xref ref-type="bibr" rid="B9">2006a</xref>).</p><p>In order to develop a tool for visualization and understanding of the 3D relationships of the basal ganglia, thalamus, and basal forebrain, two atlas data sets were derived from the contours manually defined on the original histological data. The first, a voxel-based atlas, was created with labels assigned to each voxel of the reconstructed histological volume, facilitating investigation of the nuclear boundaries when navigating through the transverse, sagittal, or coronal slices of the volume (Figures <xref ref-type="fig" rid="F2">2</xref>A–D). The second is a geometric atlas which extracts structures using a marching cubes algorithm (Cline et al., <xref ref-type="bibr" rid="B14">1987</xref>), and enables visualization of the 3D relationship of subcortical nuclei and tracts. The result is a volumetric 3D atlas with 105 separately labeled structures including the basal ganglia, thalamus, subthalamic area, basal forebrain, and temporal lobe (Figure <xref ref-type="fig" rid="F2">2</xref>I).</p><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Different 3D atlas representations and integration with a high-contrast, high-resolution MRI (Colin27) (A)</bold>. Histological volume created from the original coronal data <bold>(C)</bold>. Axial reconstruction of the histological volume created from the original coronal brain slices <bold>(B)</bold>. Coronal voxel-label atlas created from the contours identified on the histological atlas <bold>(D)</bold>. Reformatted axial views created from the 3D voxel-label atlas <bold>(E,G)</bold>. Pseudo-MRI from original coronal data <bold>(E)</bold>, with a reformatted axial view <bold>(G)</bold>. The pseudo-MRI is created by modifying the intensity of the labels in the voxel-label atlas <bold>(B)</bold> to a high-contrast, high-resolution MRI templates <bold>(F,H)</bold> The pseudo-MRI is then used to estimate a non-linear transformation which matches the atlas to a high-resolution template MRI volume, or directly to a patient or participant's MRI <bold>(I)</bold>. 3D geometric atlas created from the 3D surface rendering of labels in the voxel-label atlas <bold>(B)</bold>.</p></caption><graphic xlink:href="fnsys-05-00071-g002"></graphic></fig><p>Once the 3D voxel-based atlas was completed, two separate methods were used to integrate the atlas to a patient or participant MRI (Holmes et al., <xref ref-type="bibr" rid="B32">1998</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B12">2008</xref>). In the first strategy, also used in our initial atlas (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>), multiple homologous points were identified in the atlas and on the Colin27 MRI. An affine transformation was then used to fit the atlas to the Colin27 MRI. ANIMAL can then be used to aid in atlas integration with the patient or participant MRI. In a second strategy, a novel pseudo-MRI (Figures <xref ref-type="fig" rid="F2">2</xref>E,G) was created by matching the intensity of basal ganglia nuclei, thalamus, and internal capsule in the voxel-label atlas (Figures <xref ref-type="fig" rid="F2">2</xref>B,D) to the corresponding structures on Colin27 MRI (Figures <xref ref-type="fig" rid="F2">2</xref>F,H). The pseudo-MRI atlas is then warped to the Colin27 brain using ANIMAL. The same transform is then applied to the voxel-based atlas, resulting in integration of the atlas with the Colin27 template. The resulting atlas-integrated Colin27 MRI can then be warped to the target patient MRI using standard MRI-to-MRI non-linear registration techniques such as the ANIMAL algorithm. As an alternative, the pseudo-MRI can be directly integrated with the patient MRI, with comparable results (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B12">2008</xref>).</p></sec><sec><title>Applications of the atlases</title><p>The two atlases have been adapted to a number of applications in human, including incorporation with a surgical planning platform (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>), analysis of microelectrode responses in the subthalamic nucleus during cortical transcranial magnetic stimulation (Strafella et al., <xref ref-type="bibr" rid="B58">2004</xref>), analysis of fMRI–EEG data in patients with epilepsy (Tyvaert et al., <xref ref-type="bibr" rid="B61">2009</xref>), confirming the stereotactic position of the sensory thalamus (Figures <xref ref-type="fig" rid="F3">3</xref>A–F) by correlating the atlas with stimulation induced sensory responses (Chakravarty et al., <xref ref-type="bibr" rid="B11">2005</xref>, <xref ref-type="bibr" rid="B12">2008</xref>). The atlases have also been used to clarify the location of effective thalamic lesions for medically intractable tremor, and in determining the position of deep brain stimulation electrodes (Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>). Display of lesions, or active electrode contacts from multiple patients, in a common probabilistic atlas-integrated space, allows for statistical analysis of differences in clinical outcome. For example, our recent analysis of (Chakravarty et al., <xref ref-type="bibr" rid="B10">2006b</xref>) motor outcome after subthalamic stimulation indicates that the most effective electrodes for relief of appendicular manifestations of Parkinson's disease (Figures <xref ref-type="fig" rid="F4">4</xref>A–C) are located in the posterior and lateral part of the subthalamic nucleus, and dorsal to the nucleus, in the region of the zona incerta and ventral thalamus (Chakravarty et al., <xref ref-type="bibr" rid="B10">2006b</xref>; Sadikot et al., <xref ref-type="bibr" rid="B52">2006</xref>).</p><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>(A–D)</bold> Voxel-label atlas of the basal ganglia and thalamus integrated into a high-contrast high-resolution MRI (Colin27). <bold>(E,F)</bold> The sensory thalamus is isolated in the atlas and represented on coronal and sagittal views. The average stereotactic position of the somatosensory responses obtained during stereotactic neurosurgery in the thalamus from nine patients is integrated into the same MRI. The somatosensory responses were obtained using a curved retractable stimulator, and the position of hand/arm area responses from multiple patients was analyzed in the atlas-integrated reference space. The circle represents the 90% probability map of somatosensory responses, which map to the rostral portion of the ventral posterior somatosensory nucleus of the thalamus.</p></caption><graphic xlink:href="fnsys-05-00071-g003"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><p><bold>(A)</bold> Post-operative sagittal T1-weighted MRI scan of a patient who underwent insertion of subthalamic stimulators for Parkinson's disease. The hypointense signal artifact shows the four electrode contacts (Medtronic 3387) that traverse the subthalamic nucleus, identified during surgery using an array of five microelectrodes (“Ben's Gun” array). The electrode contacts are within, and dorsal to the subthalamic nucleus. Abbreviations: cc, corpus callosum; Cd, caudate; Th, thalamus. <bold>(B)</bold> The automatic non-linear image matching and automatic labeling (ANIMAL) algorithm was used to integrate each patent's MRI scan with the canonical high-resolution MRI (Colin27), resulting in a common space for evaluation of electrode positions from different patients. A probabilistic average map of active contacts of subthalamic stimulators associated with the best outcome for motor symptoms of the contralateral side is shown. <bold>(C)</bold> The voxel-labeled 3D atlas was integrated with the probabilistic volume map of the most effective active electrode contacts in patients with Parkinson's disease with subthalamic stimulator implants. The subthalamic nucleus is represented as a net. A 90% probability map of most effective electrode positions shows they are localized in the dorsolateral subthalamic nucleus, and areas dorsal and posterior to the subthalamic nucleus, including the zona incerta, Forel's fields, and ventral thalamus.</p></caption><graphic xlink:href="fnsys-05-00071-g004"></graphic></fig><p>In addition to surgical targeting, the VIPER platform provides a useful method for virtual <italic>in vivo</italic> “histological” analysis of effective and less effective lesions or DBS lead positions for tremor (Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>). The MRI-integrated reference atlas was also used to display electrophysiological responses from the internal capsule or the subthalamic nucleus in a common reference space (Strafella et al., <xref ref-type="bibr" rid="B58">2004</xref>; Duerden et al., <xref ref-type="bibr" rid="B17">2011</xref>). Finally, the atlases are also used in analysis of subcortical functional activation in multiple modalities, including PET and fMRI. For example, the atlas was recently used to demonstrate that activation of intralaminar nuclei occurs prior to anterior thalamic nuclei in patients with generalized spike and wave epilepsy studied by fMRI–EEG (Tyvaert et al., <xref ref-type="bibr" rid="B61">2009</xref>).</p></sec></sec><sec sec-type="discussion"><title>Discussion</title><p>When digital atlases were first used for integration with patient's stereotactic ventriculograms, CT scans, or MRI scans, linear transformations mapping the atlas to patient data were estimated to register an atlas to an individual patient scan (Bertrand et al., <xref ref-type="bibr" rid="B6">1973</xref>; Hardy et al., <xref ref-type="bibr" rid="B23">1980a</xref>,<xref ref-type="bibr" rid="B24">b</xref>, <xref ref-type="bibr" rid="B25">1981</xref>; Yoshida, <xref ref-type="bibr" rid="B69">1987</xref>; Yeo and Nowinski, <xref ref-type="bibr" rid="B68">1997</xref>). Atlas integration by simple linear scaling of axial, sagittal, or coronal data sets is limited by the fact that the three planes are necessarily derived from different hemispheres of different individuals. This results in variations of the position of structures in stereotaxic space (Niemann and van Nieuwenhofen, <xref ref-type="bibr" rid="B43">1999</xref>; Nowinski, <xref ref-type="bibr" rid="B44">2004</xref>; Nowinski et al., <xref ref-type="bibr" rid="B48">2007</xref>), which is especially important to note when attempting to scale the three representations of nuclear structures into the triplanar MRI space of a patient or individual participant. Attempts at creating 3D atlas versions from histological data are limited by the quality, triplanar anatomical correspondence, and resolution of the initial data set. We have developed methods for partially correcting for artifacts resulting from variations in staining intensity, shear, and inter-slice distance variations, allowing creation of a lower resolution 3D data set based on the Schaltenbrand and Wahren Atlas. The missing inter-slice data in the original data set was accounted for using Hermite cubic polynomials allowed for creation of smooth 3D structures. The lower resolution 3D atlas was integrated to a stereotactic platform that allows surgical tool representation and creation of virtual lesions in atlas space. The utility of computerized 3D atlases can be limited by the accuracy of the method used for integration into patient or participant target imaging. In order to overcome the limitations of linear scaling methods used for atlas integration into patient data, our group was one of the first to apply non-linear transformations which warp a digital atlas to fit pre-operative or post-operative patient MRI data, accounting for local variations in the anatomy (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>; Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>).</p><p>To improve atlas resolution, we created a new high-resolution 3D data set from histological data from a middle-aged man who died from a non-neurological cause. Thalamic atlases, especially those created for stereotactic neurosurgery, mainly use Hassler's detailed parcellation of the thalamus. More recent work has emphasized homologies between parcellations in non-human primates and humans (Jones, <xref ref-type="bibr" rid="B33">2007</xref>). In the work of Hirai and Jones, cytoarchitecture and tract-tracing data based on connections of the monkey thalamus, were harmonized with that of human thalamic parcellation based on myelo-architecture and histochemical stains (Walker, <xref ref-type="bibr" rid="B65">1938</xref>; Hirai and Jones, <xref ref-type="bibr" rid="B31">1989b</xref>; Jones, <xref ref-type="bibr" rid="B33">2007</xref>). In creating our higher resolution 3D atlas, we therefore undertook to present nomenclature using both commonly applied terminologies, allowing precise 2D and 3D homology between the nomenclature used by the Hassler school and that of Jones and Hirai. We also compared terminologies for basal forebrain and amygdala nuclei used in the Schaltenbrand atlas (Schaltenbrand and Wahren, <xref ref-type="bibr" rid="B55">1977</xref>), with the more recent atlas of Paxinos and Mai (Mai et al., <xref ref-type="bibr" rid="B39">2008</xref>), and the work of Brockhaus (Gloor, <xref ref-type="bibr" rid="B19">1997</xref>). To date, our atlas boundaries are derived from myelin and Nissl stains. Other authors have provided important additional data sets based on chemical anatomy, particularly the calcium binding proteins, which provide useful additional information compared to traditional cytoarchitectonic and histochemical parcellations (Morel et al., <xref ref-type="bibr" rid="B41">1997</xref>; Mai et al., <xref ref-type="bibr" rid="B38">2004</xref>, <xref ref-type="bibr" rid="B39">2008</xref>; Yelnik et al., <xref ref-type="bibr" rid="B66">2007</xref>; Bhattacharjee et al., <xref ref-type="bibr" rid="B7">2008</xref>; Bardinet et al., <xref ref-type="bibr" rid="B4">2009</xref>; Krauth et al., <xref ref-type="bibr" rid="B36">2010</xref>).</p><p>Many groups use template based procedures to warp atlases to pre-operative patient data. Once the atlas has been customized to an MRI, a non-linear transformation can be estimated to match the anatomy between the atlas and the template. Essentially, the atlas matching problem is then simplified to the standard MRI-to-MRI non-linear registration problem (Chakravarty et al., <xref ref-type="bibr" rid="B13">2009</xref>). For example, D'Haese et al. developed a combined anatomical and electrophysiological atlas (D′Haese et al., <xref ref-type="bibr" rid="B16">2005</xref>; Pallavaram et al., <xref ref-type="bibr" rid="B50">2010</xref>) which integrated subcortical delineations and electrophysiological intraoperative recordings from the subthalamic nucleus registered to a template created from the average of pre-operative data. This group noted that the choice of template was crucial for the accuracy of subsequent atlas customization due to the differing underlying anatomies between populations suffering from neurodegenerative diseases and the template. Other groups have suggested that non-linear transformations should be used with caution in the atlas customization procedure as they may abnormally deform the morphology of the subcortical neuroanatomy (Yelnik et al., <xref ref-type="bibr" rid="B66">2007</xref>; Bardinet et al., <xref ref-type="bibr" rid="B4">2009</xref>). Their work uses histological and MRI data prospectively acquired from a single subject, and they demonstrate impressive target-localization accuracy using only affine transformations. The work of these authors has been validated using intraoperative recordings and post-operative electrode location.</p><p>Work from our group argues that non-linear transformations alone may be suboptimal for pre-operative atlas-based target identification (Chakravarty et al., <xref ref-type="bibr" rid="B13">2009</xref>). Pre-operative planning is limited by the accuracy of the warping techniques used. Validation of non-linear registration algorithms is a notoriously difficult problem given the lack of a universally accepted “gold-standard” (Chakravarty et al., <xref ref-type="bibr" rid="B13">2009</xref>; Klein et al., <xref ref-type="bibr" rid="B35">2009</xref>). Many groups simply use anatomical correspondence between intraoperative recordings and post-operative electrode locations to validate their findings. However, we propose it is important to borrow heavily from the medical image processing community where several methods have been proposed for the validation of non-linear registration algorithms (Hellier et al., <xref ref-type="bibr" rid="B29">2003</xref>; Robbins et al., <xref ref-type="bibr" rid="B51">2004</xref>; Chakravarty et al., <xref ref-type="bibr" rid="B13">2009</xref>; Klein et al., <xref ref-type="bibr" rid="B35">2009</xref>).</p><p>We have applied our atlases to a wide variety of applications, including use in a stereotactic planning platform (St-Jean et al., <xref ref-type="bibr" rid="B57">1998</xref>), probabilistic analysis of thalamic lesions used for alleviation of tremor (Atkinson et al., <xref ref-type="bibr" rid="B3">2002</xref>), analysis of the stereotactic location of the human sensory thalamus using information obtained during intraoperative stimulation (Figures <xref ref-type="fig" rid="F3">3</xref>E,F) or following activation visualized by functional brain imaging (Chakravarty et al., <xref ref-type="bibr" rid="B12">2008</xref>), probabilistic analysis of the topography and location of motor fibers of the posterior limb of the internal capsule obtained using intraoperative stimulation (Duerden et al., <xref ref-type="bibr" rid="B17">2011</xref>), and probabilistic analysis of the location of effective and less effective subthalamic nucleus stimulation electrodes (Chakravarty et al., <xref ref-type="bibr" rid="B10">2006b</xref>; Sadikot et al., <xref ref-type="bibr" rid="B52">2006</xref>). Ongoing work includes further application of the atlas to functional neurosurgery, analysis of positions of subcortical lesions or electrodes, interpretation of subcortical functional activation data, and use with <italic>in vivo</italic> tractography. Future work by our group and many others, will involve creation of additional computerized atlases based on diverse chemical anatomy data, and atlas integration with functional data obtained using functional brain imaging, physiological responses obtained during neurosurgery, or with anatomical tractography information.</p></sec><sec><title>Conflict of Interest Statement</title><p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p></sec></body><back><ack><p>This work was supported by grants to Abbas F. Sadikot and D. Louis Collins from the CIHR and NSERC.</p></ack><ref-list><title>References</title><ref id="B1"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Afshar</surname><given-names>F.</given-names></name><name><surname>Watkins</surname><given-names>E. S.</given-names></name><name><surname>Yap</surname><given-names>J. C.</given-names></name></person-group> (<year>1978</year>). <source>Stereotaxic Atlas of the Human Brainstem and Cerebellar Nuclei: A Variability Study</source>. <publisher-loc>New York</publisher-loc>: <publisher-name>Raven Press</publisher-name></mixed-citation></ref><ref id="B2"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Andrew</surname><given-names>J.</given-names></name><name><surname>Tomlinson</surname><given-names>J. D. W.</given-names></name><name><surname>Watkins</surname><given-names>E. S.</given-names></name></person-group> (<year>1969</year>). <source>A Stereotaxic Atlas of the Human Thalamus and Adjacent Structures: A Variability Study</source>. <publisher-loc>Baltimore</publisher-loc>: <publisher-name>Williams & Wilkins</publisher-name></mixed-citation></ref><ref id="B3"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Atkinson</surname><given-names>J. D.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Peters</surname><given-names>T. M.</given-names></name><name><surname>Pike</surname><given-names>G. B.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name></person-group> (<year>2002</year>). <article-title>Optimal location of thalamotomy lesions for tremor associated with Parkinson disease: a probabilistic analysis based on postoperative magnetic resonance imaging and an integrated digital atlas</article-title>. <source>J. Neurosurg.</source> <volume>96</volume>, <fpage>854</fpage>–<lpage>866</lpage><pub-id pub-id-type="doi">10.3171/jns.2002.96.5.0854</pub-id><pub-id pub-id-type="pmid">12005392</pub-id></mixed-citation></ref><ref id="B4"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bardinet</surname><given-names>E.</given-names></name><name><surname>Bhattacharjee</surname><given-names>M.</given-names></name><name><surname>Dormont</surname><given-names>D.</given-names></name><name><surname>Pidoux</surname><given-names>B.</given-names></name><name><surname>Malandain</surname><given-names>G.</given-names></name><name><surname>Schupbach</surname><given-names>M.</given-names></name><name><surname>Ayache</surname><given-names>N.</given-names></name><name><surname>Cornu</surname><given-names>P.</given-names></name><name><surname>Agid</surname><given-names>Y.</given-names></name><name><surname>Yelnik</surname><given-names>J.</given-names></name></person-group> (<year>2009</year>). <article-title>A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease</article-title>. <source>J. Neurosurg.</source> <volume>110</volume>, <fpage>208</fpage>–<lpage>219</lpage><pub-id pub-id-type="doi">10.3171/2008.3.17469</pub-id><pub-id pub-id-type="pmid">18976051</pub-id></mixed-citation></ref><ref id="B5"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Berks</surname><given-names>G.</given-names></name><name><surname>Pohl</surname><given-names>G.</given-names></name><name><surname>Keyserlingk</surname><given-names>D. G.</given-names></name></person-group> (<year>2001</year>). <article-title>3D-VIEWER: an atlas-based system for individual and statistical investigations of the human brain</article-title>. <source>Methods Inf. Med.</source> <volume>40</volume>, <fpage>170</fpage>–<lpage>177</lpage><pub-id pub-id-type="pmid">11501628</pub-id></mixed-citation></ref><ref id="B6"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Oliver</surname><given-names>A.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1973</year>). <article-title>The computerized brain atlas: its use in stereotaxic surgery</article-title>. <source>Trans. Am. Neurol. Assoc.</source> <volume>98</volume>, <fpage>233</fpage><pub-id pub-id-type="pmid">4594187</pub-id></mixed-citation></ref><ref id="B7"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bhattacharjee</surname><given-names>M.</given-names></name><name><surname>Pitiot</surname><given-names>A.</given-names></name><name><surname>Roche</surname><given-names>A.</given-names></name><name><surname>Dormont</surname><given-names>D.</given-names></name><name><surname>Bardinet</surname><given-names>E.</given-names></name></person-group> (<year>2008</year>). <article-title>Anatomy-preserving nonlinear registration of deep brain ROIs using confidence-based block-matching</article-title>. <source>Med. Image Comput. Comput. Assist. Interv.</source> <volume>11</volume>, <fpage>956</fpage>–<lpage>963</lpage><pub-id pub-id-type="pmid">18982697</pub-id></mixed-citation></ref><ref id="B8"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bookstein</surname><given-names>F. L.</given-names></name></person-group> (<year>1989</year>). <article-title>Principal warps – thin-plate splines and the decomposition of deformations</article-title>. <source>IEEE Trans. Pattern Anal. Mach. Intell.</source> <volume>11</volume>, <fpage>567</fpage>–<lpage>585</lpage><pub-id pub-id-type="doi">10.1109/34.24792</pub-id></mixed-citation></ref><ref id="B9"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakravarty</surname><given-names>M. M.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Hodge</surname><given-names>C. P.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name></person-group> (<year>2006a</year>). <article-title>The creation of a brain atlas for image guided neurosurgery using serial histological data</article-title>. <source>Neuroimage</source> <volume>30</volume>, <fpage>359</fpage>–<lpage>376</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2005.09.041</pub-id><pub-id pub-id-type="pmid">16406816</pub-id></mixed-citation></ref><ref id="B10"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakravarty</surname><given-names>M. M.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Mongia</surname><given-names>S.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name></person-group> (<year>2006b</year>). <article-title>Towards a multi-modal atlas for neurosurgical planning</article-title>. <source>Med. Image Comput. Comput. Assist. Interv.</source> <volume>9</volume>, <fpage>389</fpage>–<lpage>396</lpage><pub-id pub-id-type="pmid">17354796</pub-id></mixed-citation></ref><ref id="B11"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakravarty</surname><given-names>M. M.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Germann</surname><given-names>J.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name></person-group> (<year>2005</year>). <article-title>Anatomical and electrophysiological validation of an atlas for neurosurgical planning</article-title>. <source>Med. Image Comput. Comput. Assist. Interv.</source> <volume>8</volume>, <fpage>394</fpage>–<lpage>401</lpage><pub-id pub-id-type="pmid">16685984</pub-id></mixed-citation></ref><ref id="B12"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakravarty</surname><given-names>M. M.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Germann</surname><given-names>J.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name></person-group> (<year>2008</year>). <article-title>Towards a validation of atlas warping techniques</article-title>. <source>Med. Image Anal.</source> <volume>12</volume>, <fpage>713</fpage>–<lpage>726</lpage><pub-id pub-id-type="doi">10.1016/j.media.2008.04.003</pub-id><pub-id pub-id-type="pmid">18640867</pub-id></mixed-citation></ref><ref id="B13"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chakravarty</surname><given-names>M. M.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Germann</surname><given-names>J.</given-names></name><name><surname>Hellier</surname><given-names>P.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name></person-group> (<year>2009</year>). <article-title>Comparison of piece-wise linear, linear, and nonlinear atlas-to-patient warping techniques: analysis of the labeling of subcortical nuclei for functional neurosurgical applications</article-title>. <source>Hum. Brain Mapp.</source> <volume>30</volume>, <fpage>3574</fpage>–<lpage>3595</lpage><pub-id pub-id-type="doi">10.1002/hbm.20598</pub-id><pub-id pub-id-type="pmid">19387981</pub-id></mixed-citation></ref><ref id="B14"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cline</surname><given-names>H. E.</given-names></name><name><surname>Dumoulin</surname><given-names>C. L.</given-names></name><name><surname>Hart</surname><given-names>H. R.</given-names><suffix>Jr.</suffix></name><name><surname>Lorensen</surname><given-names>W. E.</given-names></name><name><surname>Ludke</surname><given-names>S.</given-names></name></person-group> (<year>1987</year>). <article-title>3D reconstruction of the brain from magnetic resonance images using a connectivity algorithm</article-title>. <source>Magn. Reson. Imaging</source> <volume>5</volume>, <fpage>345</fpage>–<lpage>352</lpage><pub-id pub-id-type="doi">10.1016/0730-725X(87)90124-X</pub-id><pub-id pub-id-type="pmid">3695821</pub-id></mixed-citation></ref><ref id="B15"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Collins</surname><given-names>D. L.</given-names></name><name><surname>Evans</surname><given-names>A. C.</given-names></name><name><surname>Holmes</surname><given-names>C.</given-names></name><name><surname>Peters</surname><given-names>T. M.</given-names></name></person-group> (<year>1995</year>). <article-title>Automatic 3D segmentation of neuro-anatomical structures from MRI</article-title>. <source>Inf. Process. Med. Imaging</source> <volume>3</volume>, <fpage>139</fpage>–<lpage>152</lpage></mixed-citation></ref><ref id="B16"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>D'Haese</surname><given-names>P. F.</given-names></name><name><surname>Cetinkaya</surname><given-names>E.</given-names></name><name><surname>Konrad</surname><given-names>P. E.</given-names></name><name><surname>Kao</surname><given-names>C.</given-names></name><name><surname>Dawant</surname><given-names>B. M.</given-names></name></person-group> (<year>2005</year>). <article-title>Computer-aided placement of deep brain stimulators: from planning to intraoperative guidance</article-title>. <source>IEEE Trans. Med. Imaging</source> <volume>24</volume>, <fpage>1469</fpage>–<lpage>1478</lpage><pub-id pub-id-type="doi">10.1109/TMI.2005.856752</pub-id><pub-id pub-id-type="pmid">16279083</pub-id></mixed-citation></ref><ref id="B17"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Duerden</surname><given-names>E. G.</given-names></name><name><surname>Finnis</surname><given-names>K. W.</given-names></name><name><surname>Peters</surname><given-names>T. M.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name></person-group> (<year>2011</year>). <article-title>Three-dimensional somatotopic organization and probabilistic mapping of motor responses from the human internal capsule</article-title>. <source>J. Neurosurg.</source> <volume>114</volume>, <fpage>1706</fpage>–<lpage>1714</lpage><pub-id pub-id-type="doi">10.3171/2011.1.JNS10136</pub-id><pub-id pub-id-type="pmid">21375376</pub-id></mixed-citation></ref><ref id="B18"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Duval</surname><given-names>C.</given-names></name><name><surname>Panisset</surname><given-names>M.</given-names></name><name><surname>Strafella</surname><given-names>A. P.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name></person-group> (<year>2006</year>). <article-title>The impact of ventrolateral thalamotomy on tremor and voluntary motor behavior in patients with Parkinson's disease</article-title>. <source>Exp. Brain Res.</source> <volume>170</volume>, <fpage>160</fpage>–<lpage>171</lpage><pub-id pub-id-type="doi">10.1007/s00221-005-0198-4</pub-id><pub-id pub-id-type="pmid">16328283</pub-id></mixed-citation></ref><ref id="B19"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Gloor</surname><given-names>P.</given-names></name></person-group> (<year>1997</year>). <source>The Temporal Lobe and Limbic System</source>. <publisher-loc>New York</publisher-loc>: <publisher-name>Oxford University Press</publisher-name></mixed-citation></ref><ref id="B20"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1979a</year>). <article-title>The position and organization of motor fibers in the internal capsule found during stereotactic surgery</article-title>. <source>Appl. Neurophysiol.</source> <volume>42</volume>, <fpage>160</fpage>–<lpage>170</lpage><pub-id pub-id-type="pmid">380467</pub-id></mixed-citation></ref><ref id="B21"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1979b</year>). <article-title>Thalamic recordings during stereotactic surgery. I. Surgery topography of evoked and nonevoked rhythmic cellular activity</article-title>. <source>Appl. Neurophysiol.</source> <volume>42</volume>, <fpage>185</fpage>–<lpage>197</lpage><pub-id pub-id-type="pmid">378124</pub-id></mixed-citation></ref><ref id="B22"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1979c</year>). <article-title>Thalamic recordings during stereotactic surgery. II. Location of quick-adapting touch-evoked (novelty) cellular responses</article-title>. <source>Appl. Neurophysiol.</source> <volume>42</volume>, <fpage>198</fpage>–<lpage>202</lpage><pub-id pub-id-type="pmid">453811</pub-id></mixed-citation></ref><ref id="B23"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1980a</year>). <article-title>Organization and topography of sensory responses in the internal capsule and nucleus ventralis caudalis found during stereotactic surgery</article-title>. <source>Appl. Neurophysiol.</source> <volume>42</volume>, <fpage>335</fpage>–<lpage>351</lpage><pub-id pub-id-type="pmid">6990862</pub-id></mixed-citation></ref><ref id="B24"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1980b</year>). <article-title>Position and organization of thalamic cellular activity during diencephalic recording. I. Pressure-evoked activity</article-title>. <source>Appl. Neurophysiol.</source> <volume>43</volume>, <fpage>18</fpage>–<lpage>27</lpage><pub-id pub-id-type="pmid">7469401</pub-id></mixed-citation></ref><ref id="B25"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Bertrand</surname><given-names>G.</given-names></name><name><surname>Thompson</surname><given-names>C. J.</given-names></name></person-group> (<year>1981</year>). <article-title>Touch-evoked thalamic cellular activity. The variable position of the anterior border of somesthetic SI thalamus and somatotopography</article-title>. <source>Appl. Neurophysiol.</source> <volume>44</volume>, <fpage>302</fpage>–<lpage>313</lpage><pub-id pub-id-type="pmid">7051974</pub-id></mixed-citation></ref><ref id="B26"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hardy</surname><given-names>T. L.</given-names></name><name><surname>Smith</surname><given-names>J. R.</given-names></name><name><surname>Brynildson</surname><given-names>L. R.</given-names></name><name><surname>Flanigan</surname><given-names>H. F.</given-names></name><name><surname>Gray</surname><given-names>J. G.</given-names></name><name><surname>Spurlock</surname><given-names>D.</given-names></name></person-group> (<year>1992</year>). <article-title>Magnetic resonance imaging and anatomic atlas mapping for thalamotomy</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>58</volume>, <fpage>30</fpage>–<lpage>32</lpage><pub-id pub-id-type="doi">10.1159/000098987</pub-id><pub-id pub-id-type="pmid">1439345</pub-id></mixed-citation></ref><ref id="B27"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hassler</surname><given-names>R.</given-names></name><name><surname>Mundinger</surname><given-names>F.</given-names></name><name><surname>Riechert</surname><given-names>T.</given-names></name></person-group> (<year>1965</year>). <article-title>Correlations between clinical and autoptic findings in stereotaxic operations of parkinsonism</article-title>. <source>Confin. Neurol.</source> <volume>26</volume>, <fpage>282</fpage>–<lpage>290</lpage><pub-id pub-id-type="pmid">5329830</pub-id></mixed-citation></ref><ref id="B28"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Heimer</surname><given-names>L.</given-names></name><name><surname>Harlan</surname><given-names>R. E.</given-names></name><name><surname>Alheid</surname><given-names>G. F.</given-names></name><name><surname>Garcia</surname><given-names>M. M.</given-names></name><name><surname>de Olmos</surname><given-names>J.</given-names></name></person-group> (<year>1997</year>). <article-title>Substantia innominata: a notion which impedes clinical-anatomical correlations in neuropsychiatric disorders</article-title>. <source>Neuroscience</source> <volume>76</volume>, <fpage>957</fpage>–<lpage>1006</lpage><pub-id pub-id-type="doi">10.1016/S0306-4522(96)00405-8</pub-id><pub-id pub-id-type="pmid">9027863</pub-id></mixed-citation></ref><ref id="B29"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hellier</surname><given-names>P.</given-names></name><name><surname>Barillot</surname><given-names>C.</given-names></name><name><surname>Corouge</surname><given-names>I.</given-names></name><name><surname>Gibaud</surname><given-names>B.</given-names></name><name><surname>Le Goualher</surname><given-names>G.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name><name><surname>Evans</surname><given-names>A.</given-names></name><name><surname>Malandain</surname><given-names>G.</given-names></name><name><surname>Ayache</surname><given-names>N.</given-names></name><name><surname>Christensen</surname><given-names>G. E.</given-names></name><name><surname>Johnson</surname><given-names>H. J.</given-names></name></person-group> (<year>2003</year>). <article-title>Retrospective evaluation of intersubject brain registration</article-title>. <source>IEEE Trans. Med. Imaging</source> <volume>22</volume>,<fpage>1120</fpage>–<lpage>1130</lpage><pub-id pub-id-type="doi">10.1109/TMI.2002.808365</pub-id><pub-id pub-id-type="pmid">12956267</pub-id></mixed-citation></ref><ref id="B30"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hirai</surname><given-names>T.</given-names></name><name><surname>Jones</surname><given-names>E. G.</given-names></name></person-group> (<year>1989a</year>). <article-title>Distribution of tachykinin- and enkephalin-immunoreactive fibers in the human thalamus</article-title>. <source>Brain Res. Brain Res. Rev.</source> <volume>14</volume>, <fpage>35</fpage>–<lpage>52</lpage><pub-id pub-id-type="doi">10.1016/0165-0173(89)90007-6</pub-id><pub-id pub-id-type="pmid">2720230</pub-id></mixed-citation></ref><ref id="B31"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hirai</surname><given-names>T.</given-names></name><name><surname>Jones</surname><given-names>E. G.</given-names></name></person-group> (<year>1989b</year>). <article-title>A new parcellation of the human thalamus on the basis of histochemical staining</article-title>. <source>Brain Res. Brain Res. Rev.</source> <volume>14</volume>, <fpage>1</fpage>–<lpage>34</lpage><pub-id pub-id-type="doi">10.1016/0165-0173(89)90007-6</pub-id><pub-id pub-id-type="pmid">2720229</pub-id></mixed-citation></ref><ref id="B32"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Holmes</surname><given-names>C. J.</given-names></name><name><surname>Hoge</surname><given-names>R.</given-names></name><name><surname>Collins</surname><given-names>L.</given-names></name><name><surname>Woods</surname><given-names>R.</given-names></name><name><surname>Toga</surname><given-names>A. W.</given-names></name><name><surname>Evans</surname><given-names>A. C.</given-names></name></person-group> (<year>1998</year>). <article-title>Enhancement of MR images using registration for signal averaging</article-title>. <source>J. Comput. Assist. Tomogr.</source> <volume>22</volume>, <fpage>324</fpage>–<lpage>333</lpage><pub-id pub-id-type="doi">10.1097/00004728-199803000-00032</pub-id><pub-id pub-id-type="pmid">9530404</pub-id></mixed-citation></ref><ref id="B33"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Jones</surname><given-names>E. G.</given-names></name></person-group> (<year>2007</year>). <source>The Thalamus</source>. <publisher-loc>Cambridge, NY</publisher-loc>: <publisher-name>Cambridge University Press</publisher-name></mixed-citation></ref><ref id="B34"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kazarnovskaya</surname><given-names>M. I.</given-names></name><name><surname>Borodkin</surname><given-names>S. M.</given-names></name><name><surname>Shabalov</surname><given-names>V. A.</given-names></name><name><surname>Krivosheina</surname><given-names>V. Y.</given-names></name><name><surname>Golanov</surname><given-names>A. V.</given-names></name></person-group> (<year>1991</year>). <article-title>3-D computer model of subcortical structures of human brain</article-title>. <source>Comput. Biol. Med.</source> <volume>21</volume>, <fpage>451</fpage>–<lpage>417</lpage><pub-id pub-id-type="doi">10.1016/0010-4825(91)90047-D</pub-id><pub-id pub-id-type="pmid">1790690</pub-id></mixed-citation></ref><ref id="B35"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Klein</surname><given-names>A.</given-names></name><name><surname>Andersson</surname><given-names>J.</given-names></name><name><surname>Ardekani</surname><given-names>B. A.</given-names></name><name><surname>Ashburner</surname><given-names>J.</given-names></name><name><surname>Avants</surname><given-names>B.</given-names></name><name><surname>Chiang</surname><given-names>M. C.</given-names></name><name><surname>Christensen</surname><given-names>G. E.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name><name><surname>Gee</surname><given-names>J.</given-names></name><name><surname>Hellier</surname><given-names>P.</given-names></name><name><surname>Song</surname><given-names>J. H.</given-names></name><name><surname>Jenkinson</surname><given-names>M.</given-names></name><name><surname>Lepage</surname><given-names>C.</given-names></name><name><surname>Rueckert</surname><given-names>D.</given-names></name><name><surname>Thompson</surname><given-names>P.</given-names></name><name><surname>Vercauteren</surname><given-names>T.</given-names></name><name><surname>Woods</surname><given-names>R. P.</given-names></name><name><surname>Mann</surname><given-names>J. J.</given-names></name><name><surname>Parsey</surname><given-names>R. V.</given-names></name></person-group> (<year>2009</year>). <article-title>Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration</article-title>. <source>Neuroimage</source> <volume>46</volume>, <fpage>786</fpage>–<lpage>802</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2008.12.037</pub-id><pub-id pub-id-type="pmid">19195496</pub-id></mixed-citation></ref><ref id="B36"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Krauth</surname><given-names>A.</given-names></name><name><surname>Blanc</surname><given-names>R.</given-names></name><name><surname>Poveda</surname><given-names>A.</given-names></name><name><surname>Jeanmonod</surname><given-names>D.</given-names></name><name><surname>Morel</surname><given-names>A.</given-names></name><name><surname>Szekely</surname><given-names>G.</given-names></name></person-group> (<year>2010</year>). <article-title>A mean three-dimensional atlas of the human thalamus: generation from multiple histological data</article-title>. <source>Neuroimage</source> <volume>49</volume>, <fpage>2053</fpage>–<lpage>2062</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2009.10.042</pub-id><pub-id pub-id-type="pmid">19853042</pub-id></mixed-citation></ref><ref id="B37"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Macdonald</surname><given-names>D.</given-names></name><name><surname>Avis</surname><given-names>D.</given-names></name><name><surname>Evans</surname><given-names>A. C.</given-names></name></person-group> (<year>1994</year>). <article-title>Multiple surface identification and matching in magnetic-resonance images</article-title>. <source>Vis. Biomed. Comput.</source> <volume>2359</volume>, <fpage>160</fpage>–<lpage>169</lpage></mixed-citation></ref><ref id="B38"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Mai</surname><given-names>J. K.</given-names></name><name><surname>Assheuer</surname><given-names>J.</given-names></name><name><surname>Paxinos</surname><given-names>G.</given-names></name></person-group> (<year>2004</year>). <source>Atlas of the Human Brain</source>. <publisher-loc>Amsterdam</publisher-loc>: <publisher-name>Elsevier Academic Press</publisher-name></mixed-citation></ref><ref id="B39"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Mai</surname><given-names>J. K.</given-names></name><name><surname>Voss</surname><given-names>T.</given-names></name><name><surname>Paxinos</surname><given-names>G.</given-names></name></person-group> (<year>2008</year>). <source>Atlas of the Human Brain</source>. <publisher-loc>Amsterdam</publisher-loc>: <publisher-name>Elsevier, Academic Press</publisher-name></mixed-citation></ref><ref id="B40"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Malandain</surname><given-names>G.</given-names></name><name><surname>Bardinet</surname><given-names>E.</given-names></name><name><surname>Nelissen</surname><given-names>K.</given-names></name><name><surname>Vanduffel</surname><given-names>W.</given-names></name></person-group> (<year>2004</year>). <article-title>Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations</article-title>. <source>Neuroimage</source> <volume>23</volume>, <fpage>111</fpage>–<lpage>127</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2004.04.038</pub-id><pub-id pub-id-type="pmid">15325358</pub-id></mixed-citation></ref><ref id="B41"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Morel</surname><given-names>A.</given-names></name><name><surname>Magnin</surname><given-names>M.</given-names></name><name><surname>Jeanmonod</surname><given-names>D.</given-names></name></person-group> (<year>1997</year>). <article-title>Multiarchitectonic and stereotactic atlas of the human thalamus</article-title>. <source>J. Comp. Neurol.</source> <volume>387</volume>, <fpage>588</fpage>–<lpage>630</lpage><pub-id pub-id-type="doi">10.1002/(SICI)1096-9861(19971103)387:4<588::AID-CNE8>3.0.CO;2-Z</pub-id><pub-id pub-id-type="pmid">9373015</pub-id></mixed-citation></ref><ref id="B42"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Niemann</surname><given-names>K.</given-names></name><name><surname>Naujokat</surname><given-names>C.</given-names></name><name><surname>Pohl</surname><given-names>G.</given-names></name><name><surname>Wollner</surname><given-names>C.</given-names></name><name><surname>von Keyserlingk</surname><given-names>D.</given-names></name></person-group> (<year>1994</year>). <article-title>Verification of the Schaltenbrand and Wahren stereotactic atlas</article-title>. <source>Acta Neurochir. (Wien)</source> <volume>129</volume>, <fpage>72</fpage>–<lpage>81</lpage><pub-id pub-id-type="doi">10.1007/BF01400876</pub-id><pub-id pub-id-type="pmid">7998500</pub-id></mixed-citation></ref><ref id="B43"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Niemann</surname><given-names>K.</given-names></name><name><surname>van Nieuwenhofen</surname><given-names>I.</given-names></name></person-group> (<year>1999</year>). <article-title>One atlas – three anatomies: relationships of the Schaltenbrand and Wahren microscopic data</article-title>. <source>Acta Neurochir. (Wien)</source> <volume>141</volume>, <fpage>1025</fpage>–<lpage>1038</lpage><pub-id pub-id-type="doi">10.1007/s007010050479</pub-id><pub-id pub-id-type="pmid">10550646</pub-id></mixed-citation></ref><ref id="B44"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nowinski</surname><given-names>W. L.</given-names></name></person-group> (<year>2004</year>). <article-title>Co-registration of the Schaltenbrand-Wahren microseries with the probabilistic functional atlas</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>82</volume>, <fpage>142</fpage>–<lpage>146</lpage><pub-id pub-id-type="doi">10.1159/000081346</pub-id><pub-id pub-id-type="pmid">15467381</pub-id></mixed-citation></ref><ref id="B45"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nowinski</surname><given-names>W. L.</given-names></name><name><surname>Belov</surname><given-names>D.</given-names></name><name><surname>Thirunavuukarasuu</surname><given-names>A.</given-names></name><name><surname>Benabid</surname><given-names>A. L.</given-names></name></person-group> (<year>2005</year>). <article-title>A probabilistic functional atlas of the VIM nucleus constructed from pre-, intra- and postoperative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson's disease patients</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>83</volume>, <fpage>190</fpage>–<lpage>196</lpage><pub-id pub-id-type="doi">10.1159/000091082</pub-id><pub-id pub-id-type="pmid">16424683</pub-id></mixed-citation></ref><ref id="B46"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nowinski</surname><given-names>W. L.</given-names></name><name><surname>Fang</surname><given-names>A.</given-names></name><name><surname>Nguyen</surname><given-names>B. T.</given-names></name><name><surname>Raphel</surname><given-names>J. K.</given-names></name><name><surname>Jagannathan</surname><given-names>L.</given-names></name><name><surname>Raghavan</surname><given-names>R.</given-names></name><name><surname>Bryan</surname><given-names>R. N.</given-names></name><name><surname>Miller</surname><given-names>G. A.</given-names></name></person-group> (<year>1997</year>). <article-title>Multiple brain atlas database and atlas-based neuroimaging system</article-title>. <source>Comput. Aided Surg.</source> <volume>2</volume>, <fpage>42</fpage>–<lpage>66</lpage><pub-id pub-id-type="doi">10.3109/10929089709149082</pub-id><pub-id pub-id-type="pmid">9148878</pub-id></mixed-citation></ref><ref id="B47"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nowinski</surname><given-names>W. L.</given-names></name><name><surname>Liu</surname><given-names>J.</given-names></name><name><surname>Thirunavuukarasuu</surname><given-names>A.</given-names></name></person-group> (<year>2008</year>). <article-title>Quantification and visualization of three-dimensional inconsistency of the ventrointermediate nucleus of the thalamus in the Schaltenbrand-Wahren brain atlas</article-title>. <source>Acta Neurochir.</source> <volume>150</volume>, <fpage>647</fpage>–<lpage>653</lpage>; discussion 653.<pub-id pub-id-type="doi">10.1007/s00701-007-1270-6</pub-id></mixed-citation></ref><ref id="B48"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nowinski</surname><given-names>W. L.</given-names></name><name><surname>Thirunavuukarasuu</surname><given-names>A.</given-names></name><name><surname>Liu</surname><given-names>J.</given-names></name><name><surname>Benabid</surname><given-names>A. L.</given-names></name></person-group> (<year>2007</year>). <article-title>Correlation between the anatomical and functional human subthalamic nucleus</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>85</volume>, <fpage>88</fpage>–<lpage>93</lpage><pub-id pub-id-type="doi">10.1159/000097924</pub-id><pub-id pub-id-type="pmid">17167237</pub-id></mixed-citation></ref><ref id="B49"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Olszewski</surname><given-names>J.</given-names></name><name><surname>Baxter</surname><given-names>D. W.</given-names></name></person-group> (<year>1954</year>). <source>Cytoarchitecture of the Human Brain Stem</source>. <publisher-loc>Philadelphia</publisher-loc>: <publisher-name>Lippincott</publisher-name></mixed-citation></ref><ref id="B50"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pallavaram</surname><given-names>S.</given-names></name><name><surname>Dawant</surname><given-names>B. M.</given-names></name><name><surname>Remple</surname><given-names>M. S.</given-names></name><name><surname>Neimat</surname><given-names>J. S.</given-names></name><name><surname>Kao</surname><given-names>C.</given-names></name><name><surname>Konrad</surname><given-names>P. E.</given-names></name><name><surname>D'Haese</surname><given-names>P. F.</given-names></name></person-group> (<year>2010</year>). <article-title>Effect of brain shift on the creation of functional atlases for deep brain stimulation surgery</article-title>. <source>Int. J. Comput. Assist. Radiol. Surg.</source> <volume>5</volume>, <fpage>221</fpage>–<lpage>228</lpage><pub-id pub-id-type="doi">10.1007/s11548-009-0391-1</pub-id><pub-id pub-id-type="pmid">20033503</pub-id></mixed-citation></ref><ref id="B51"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Robbins</surname><given-names>S.</given-names></name><name><surname>Evans</surname><given-names>A. C.</given-names></name><name><surname>Collins</surname><given-names>D. L.</given-names></name><name><surname>Whitesides</surname><given-names>S.</given-names></name></person-group> (<year>2004</year>). <article-title>Tuning and comparing spatial normalization methods</article-title>. <source>Med. Image Anal.</source> <volume>8</volume>, <fpage>311</fpage>–<lpage>323</lpage><pub-id pub-id-type="doi">10.1016/j.media.2004.06.009</pub-id><pub-id pub-id-type="pmid">15450225</pub-id></mixed-citation></ref><ref id="B52"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Sadikot</surname><given-names>A.</given-names></name><name><surname>Mongia</surname><given-names>S.</given-names></name><name><surname>Chakravarty</surname><given-names>M.</given-names></name><name><surname>Panisset</surname><given-names>M.</given-names></name><name><surname>Collins</surname><given-names>D.</given-names></name></person-group> (<year>2006</year>). <source>A Novel Probabilistic Analysis of Electrode Positions in the Subthalamic Nucleus Related to Clinical Outcome</source>. <publisher-loc>San Francisco</publisher-loc>: <publisher-name>American Association of Neurological Surgeons</publisher-name></mixed-citation></ref><ref id="B53"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sather</surname><given-names>M. D.</given-names></name><name><surname>Patil</surname><given-names>A. A.</given-names></name></person-group> (<year>2007</year>). <article-title>Direct anatomical localization of the subthalamic nucleus on CT with comparison to Schaltenbrand-Wahren atlas</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>85</volume>, <fpage>1</fpage>–<lpage>5</lpage><pub-id pub-id-type="doi">10.1159/000096632</pub-id><pub-id pub-id-type="pmid">17077649</pub-id></mixed-citation></ref><ref id="B54"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Schaltenbrand</surname><given-names>G.</given-names></name><name><surname>Bailey</surname><given-names>P.</given-names></name></person-group> (<year>1959</year>). <source>Einführung in die Stereotaktischen Operationen, mit einem Atlas des menschlichen Gehirns. Introduction to Stereotaxis, with an Atlas of the Human Brain</source>. <publisher-loc>Stuttgart</publisher-loc>: <publisher-name>Thieme</publisher-name></mixed-citation></ref><ref id="B55"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Schaltenbrand</surname><given-names>G.</given-names></name><name><surname>Wahren</surname><given-names>W.</given-names></name></person-group> (<year>1977</year>). <source>Atlas for Stereotaxy of the Human Brain</source>. <publisher-loc>Chicago</publisher-loc>: <publisher-name>Year Book Medical Publishers</publisher-name></mixed-citation></ref><ref id="B56"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sramka</surname><given-names>M.</given-names></name><name><surname>Ruzicky</surname><given-names>E.</given-names></name><name><surname>Novotny</surname><given-names>M.</given-names></name></person-group> (<year>1997</year>). <article-title>Computerized brain atlas in functional neurosurgery</article-title>. <source>Stereotact. Funct. Neurosurg.</source> <volume>69</volume>, <fpage>93</fpage>–<lpage>8</lpage><pub-id pub-id-type="doi">10.1159/000099858</pub-id><pub-id pub-id-type="pmid">9711740</pub-id></mixed-citation></ref><ref id="B57"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>St-Jean</surname><given-names>P.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Collins</surname><given-names>L.</given-names></name><name><surname>Clonda</surname><given-names>D.</given-names></name><name><surname>Kasrai</surname><given-names>R.</given-names></name><name><surname>Evans</surname><given-names>A. C.</given-names></name><name><surname>Peters</surname><given-names>T. M.</given-names></name></person-group> (<year>1998</year>). <article-title>Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery</article-title>. <source>IEEE Trans. Med. Imaging</source> <volume>17</volume>, <fpage>672</fpage>–<lpage>680</lpage><pub-id pub-id-type="doi">10.1109/42.736017</pub-id><pub-id pub-id-type="pmid">9874291</pub-id></mixed-citation></ref><ref id="B58"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Strafella</surname><given-names>A. P.</given-names></name><name><surname>Vanderwerf</surname><given-names>Y.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name></person-group> (<year>2004</year>). <article-title>Transcranial magnetic stimulation of the human motor cortex influences the neuronal activity of subthalamic nucleus</article-title>. <source>Eur. J. Neurosci.</source> <volume>20</volume>, <fpage>2245</fpage>–<lpage>2249</lpage><pub-id pub-id-type="doi">10.1111/j.1460-9568.2004.03669.x</pub-id><pub-id pub-id-type="pmid">15450105</pub-id></mixed-citation></ref><ref id="B59"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Talairach</surname><given-names>J.</given-names></name></person-group> (<year>1957</year>). <source>Atlas d'anatomie stéréotaxique: repérage radiologique indirect des noyaux gris centraux des régions mésencéphalo-sous-optique et hypothalamique de l'homme</source>. <publisher-loc>Paris</publisher-loc>: <publisher-name>Masson</publisher-name></mixed-citation></ref><ref id="B60"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Talairach</surname><given-names>J.</given-names></name><name><surname>Tournoux</surname><given-names>P.</given-names></name></person-group> (<year>1988</year>). <source>Co-Planar Stereotaxic Atlas of the Human Brain: 3-Dimensional Proportional System: An Approach to Cerebral Imaging</source>. <publisher-loc>Stuttgart: G. Thieme; New York</publisher-loc>: <publisher-name>Thieme Medical Publishers</publisher-name></mixed-citation></ref><ref id="B61"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tyvaert</surname><given-names>L.</given-names></name><name><surname>Chassagnon</surname><given-names>S.</given-names></name><name><surname>Sadikot</surname><given-names>A.</given-names></name><name><surname>Levan</surname><given-names>P.</given-names></name><name><surname>Dubeau</surname><given-names>F.</given-names></name><name><surname>Gotman</surname><given-names>J.</given-names></name></person-group> (<year>2009</year>). <article-title>Thalamic nuclei activity in idiopathic generalized epilepsy: an EEG-fMRI study</article-title>. <source>Neurology</source> <volume>73</volume>, <fpage>2018</fpage>–<lpage>2022</lpage><pub-id pub-id-type="doi">10.1212/WNL.0b013e3181c55d02</pub-id><pub-id pub-id-type="pmid">19996076</pub-id></mixed-citation></ref><ref id="B62"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Van Buren</surname><given-names>J. M.</given-names></name><name><surname>Borke</surname><given-names>R. C.</given-names></name></person-group> (<year>1972</year>). <source>Variations and Connections of the Human Thalamus</source>. <publisher-loc>Berlin, NY</publisher-loc>: <publisher-name>Springer-Verlag</publisher-name></mixed-citation></ref><ref id="B63"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Buren</surname><given-names>J. M.</given-names></name><name><surname>Maccubbin</surname><given-names>D. A.</given-names></name></person-group> (<year>1962</year>). <article-title>An outline atlas of the human basal ganglia with estimation of anatomical variants</article-title>. <source>J. Neurosurg.</source> <volume>19</volume>, <fpage>811</fpage>–<lpage>839</lpage><pub-id pub-id-type="doi">10.3171/jns.1962.19.10.0811</pub-id><pub-id pub-id-type="pmid">13995970</pub-id></mixed-citation></ref><ref id="B64"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Der Werf</surname><given-names>Y. D.</given-names></name><name><surname>Sadikot</surname><given-names>A. F.</given-names></name><name><surname>Strafella</surname><given-names>A. P.</given-names></name><name><surname>Paus</surname><given-names>T.</given-names></name></person-group> (<year>2006</year>). <article-title>The neural response to transcranial magnetic stimulation of the human motor cortex. II. Thalamocortical contributions</article-title>. <source>Exp Brain Res.</source> <volume>175</volume>, <fpage>246</fpage>–<lpage>255</lpage><pub-id pub-id-type="doi">10.1007/s00221-006-0548-x</pub-id><pub-id pub-id-type="pmid">16832683</pub-id></mixed-citation></ref><ref id="B65"><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>Walker</surname><given-names>A. E.</given-names></name></person-group> (<year>1938</year>). <source>The Primate Thalamus</source>. <publisher-loc>Chicago, IL</publisher-loc>: <publisher-name>The University Press</publisher-name></mixed-citation></ref><ref id="B66"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yelnik</surname><given-names>J.</given-names></name><name><surname>Bardinet</surname><given-names>E.</given-names></name><name><surname>Dormont</surname><given-names>D.</given-names></name><name><surname>Malandain</surname><given-names>G.</given-names></name><name><surname>Ourselin</surname><given-names>S.</given-names></name><name><surname>Tande</surname><given-names>D.</given-names></name><name><surname>Karachi</surname><given-names>C.</given-names></name><name><surname>Ayache</surname><given-names>N.</given-names></name><name><surname>Cornu</surname><given-names>P.</given-names></name><name><surname>Agid</surname><given-names>Y.</given-names></name></person-group> (<year>2007</year>). <article-title>A three-dimensional, histological and deformable atlas of the human basal ganglia. I. Atlas construction based on immunohistochemical and MRI data</article-title>. <source>Neuroimage</source> <volume>34</volume>, <fpage>618</fpage>–<lpage>638</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2006.09.026</pub-id><pub-id pub-id-type="pmid">17110133</pub-id></mixed-citation></ref><ref id="B67"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yelnik</surname><given-names>J.</given-names></name><name><surname>Damier</surname><given-names>P.</given-names></name><name><surname>Bejjani</surname><given-names>B. P.</given-names></name><name><surname>Francois</surname><given-names>C.</given-names></name><name><surname>Gervais</surname><given-names>D.</given-names></name><name><surname>Dormont</surname><given-names>D.</given-names></name><name><surname>Arnulf</surname><given-names>I.</given-names></name><name><surname>Bonnet</surname><given-names>M. A.</given-names></name><name><surname>Cornu</surname><given-names>P.</given-names></name><name><surname>Pidoux</surname><given-names>B.</given-names></name><name><surname>Agid</surname><given-names>Y.</given-names></name></person-group> (<year>2000</year>). <article-title>Functional mapping of the human globus pallidus: contrasting effect of stimulation in the internal and external pallidum in Parkinson's disease</article-title>. <source>Neuroscience</source> <volume>101</volume>, <fpage>77</fpage>–<lpage>87</lpage><pub-id pub-id-type="doi">10.1016/S0306-4522(00)00364-X</pub-id><pub-id pub-id-type="pmid">11068138</pub-id></mixed-citation></ref><ref id="B68"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yeo</surname><given-names>T. T.</given-names></name><name><surname>Nowinski</surname><given-names>W. L.</given-names></name></person-group> (<year>1997</year>). <article-title>Functional neurosurgery aided by use of an electronic brain atlas</article-title>. <source>Acta Neurochir. Suppl.</source> <volume>68</volume>, <fpage>93</fpage>–<lpage>99</lpage><pub-id pub-id-type="pmid">9233422</pub-id></mixed-citation></ref><ref id="B69"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yoshida</surname><given-names>M.</given-names></name></person-group> (<year>1987</year>). <article-title>Creation of a three-dimensional atlas by interpolation from Schaltenbrand-Bailey's atlas</article-title>. <source>Appl. Neurophysiol.</source> <volume>50</volume>, <fpage>45</fpage>–<lpage>48</lpage><pub-id pub-id-type="pmid">3329879</pub-id></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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