Review of Template-Based Neuroimaging Tools in Neuro-Oncology: Novel Insights
Abstract
:Highlights
- Brain MRIs of neuro-oncology patients can be accurately transformed to MNI space.
- MNI-based studies have provided unique insights to neuro-oncology.
- While it has proven useful in other fields, it is under-utilized in neuro-oncology.
Abstract
1. Introduction
2. Methods
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Boxerman, J.L.; Quarles, C.C.; Hu, L.S.; Erickson, B.J.; Gerstner, E.R.; Smits, M.; Kaufmann, T.J.; Barboriak, D.P.; Huang, R.H.; Wick, W.; et al. Consensus recommendations for a dynamic susceptibility contrast MRI protocol for use in high-grade gliomas. Neuro-oncology 2020, 22, 1262–1275. [Google Scholar] [CrossRef] [PubMed]
- Ellingson, B.M.; Bendszus, M.; Boxerman, J.; Barboriak, D.; Erickson, B.J.; Smits, M.; Nelson, S.J.; Gerstner, E.; Alexander, B.; Goldmacher, G.; et al. Consensus recommendations for a standardized Brain Tumor Imaging Protocol in clinical trials. Neuro-oncology 2015, 17, 1188–1198. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Germann, J.; Zadeh, G.; Mansouri, A.; Kucharczyk, W.; Lozano, A.M.; Boutet, A. Untapped Neuroimaging Tools for Neuro-Oncology: Connectomics and Spatial Transcriptomics. Cancers 2022, 14, 464. [Google Scholar] [CrossRef] [PubMed]
- Avants, B.B.; Tustison, N.J.; Song, G.; Cook, P.A.; Klein, A.; Gee, J.C. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage 2011, 54, 2033–2044. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Evans, A.C.; Collins, D.L.; Milner, B. An MRI-based stereotactic atlas from 250 young normal subjects. Soc. Neurosci. Abstracts. 1992, 18, 408. [Google Scholar]
- Evans, A.; Collins, D.; Mills, S.; Brown, E.; Kelly, R.; Peters, T. 3D statistical neuroanatomical models from 305 MRI volumes. In Proceedings of the 1993 IEEE Conference Record Nuclear Science Symposium and Medical Imaging Conference, San Francisco, CA, USA, 31 October–6 November 1993. [Google Scholar] [CrossRef]
- Evans, A.C.; Marrett, S.; Neelin, P.; Collins, L.; Worsley, K.; Dai, W.; Milot, S.; Meyer, E.; Bub, D. Anatomical mapping of functional activation in stereotactic coordinate space. NeuroImage 1992, 1, 43–53. [Google Scholar] [CrossRef]
- Mazziotta, J.; Toga, A.; Evans, A.; Fox, P.; Lancaster, J.; Zilles, K.; Woods, R.; Paus, T.; Simpson, G.; Pike, B.; et al. A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM). Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 2001, 356, 1293–1322. [Google Scholar] [CrossRef]
- Fonov, V.; Evans, A.; McKinstry, R.; Almli, C.; Collins, D. Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. Neuroimage 2009, 47, S102. [Google Scholar] [CrossRef]
- Klein, A.; Andersson, J.; Ardekani, B.A.; Ashburner, J.; Avants, B.; Chiang, M.-C.; Christensen, G.E.; Collins, D.L.; Gee, J.; Hellier, P.; et al. Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage 2009, 46, 786–802. [Google Scholar] [CrossRef] [Green Version]
- Chen, H.S.; Kumar, V.A.; Johnson, J.M.; Chen, M.M.; Noll, K.R.; Hou, P.; Prabhu, S.S.; Schomer, D.F.; Liu, H. Effect of brain normalization methods on the construction of functional connectomes from resting-state functional MRI in patients with gliomas. Magn. Reson. Med. 2021, 86, 487–498. [Google Scholar] [CrossRef]
- Radwan, A.M.; Emsell, L.; Blommaert, J.; Zhylka, A.; Kovacs, S.; Theys, T.; Sollmann, N.; Dupont, P.; Sunaert, S. Virtual brain grafting: Enabling whole brain parcellation in the presence of large lesions. NeuroImage 2021, 229, 117731. [Google Scholar] [CrossRef] [PubMed]
- Weninger, L.; Gilerson, A.; Merhof, D. Improving Localization of Brain Tumors through 3D GAN Inpainting. In Proceedings of the 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Guadalajara, Mexico, 1–5 November 2021; pp. 2651–2654. [Google Scholar] [CrossRef]
- Amunts, K.; Lepage, C.; Borgeat, L.; Mohlberg, H.; Dickscheid, T.; Rousseau, M.; Bludau, S.; Bazin, P.-L.; Lewis, L.B.; Oros-Peusquens, A.-M.; et al. BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science 2013, 340, 1472–1475. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hansen, J.Y.; Shafiei, G.; Markello, R.D.; Smart, K.; Cox, S.M.L.; Nørgaard, M.; Beliveau, V.; Wu, Y.; Gallezot, J.-D.; Aumont, É.; et al. Mapping neurotransmitter systems to the structural and functional organization of the human neocortex. Nat. Neurosci. 2022, 25, 1569–1581. [Google Scholar] [CrossRef] [PubMed]
- Hill, J.; Inder, T.; Neil, J.; Dierker, D.; Harwell, J.; Van Essen, D. Similar patterns of cortical expansion during human development and evolution. Proc. Natl. Acad. Sci. USA 2010, 107, 13135–13140. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Akram, H.; Dayal, V.; Mahlknecht, P.; Georgiev, D.; Hyam, J.; Foltynie, T.; Limousin, P.; De Vita, E.; Jahanshahi, M.; Ashburner, J.; et al. Connectivity derived thalamic segmentation in deep brain stimulation for tremor. NeuroImage Clin. 2018, 18, 130–142. [Google Scholar] [CrossRef]
- Neudorfer, C.; Germann, J.; Elias, G.J.B.; Gramer, R.; Boutet, A.; Lozano, A.M. A high-resolution in vivo magnetic resonance imaging atlas of the human hypothalamic region. Sci. Data 2020, 7, 305. [Google Scholar] [CrossRef]
- Yarkoni, T.; Poldrack, R.; Nichols, T.; Van Essen, D.C.; Wager, T.D. Large-scale automated synthesis of human functional neuroimaging data. Nat. Methods 2011, 8, 665–670. [Google Scholar] [CrossRef] [Green Version]
- Thomas Yeo, B.T.; Krienen, F.M.; Sepulcre, J.; Sabuncu, M.R.; Lashkari, D.; Hollinshead, M.; Roffman, J.L.; Smoller, J.W.; Zöllei, L.; Polimeni, J.R.; et al. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J. Neurophysiol. 2011, 106, 1125–1165. [Google Scholar] [CrossRef]
- Arnatkeviciute, A.; Fulcher, B.D.; Bellgrove, M.A.; Fornito, A. Imaging Transcriptomics of Brain Disorders. Biol. Psychiatry Glob. Open Sci. 2021, 2, 319–331. [Google Scholar] [CrossRef]
- Elias, G.J.; Germann, J.; Loh, A.; Boutet, A.; Taha, A.; Wong, E.H.; Parmar, R.; Lozano, A.M. Normative connectomes and their use in DBS. In Connectomic Deep Brain Stimulation; Academic Press: Cambridge, MA, USA, 2021; pp. 245–274. [Google Scholar] [CrossRef]
- Fox, M.D. Mapping Symptoms to Brain Networks with the Human Connectome. N. Engl. J. Med. 2018, 379, 2237–2245. [Google Scholar] [CrossRef] [Green Version]
- Hawrylycz, M.J.; Lein, E.S.; Guillozet-Bongaarts, A.L.; Shen, E.H.; Ng, L.; Miller, J.A.; Van De Lagemaat, L.N.; Smith, K.A.; Ebbert, A.; Riley, Z.L.; et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 2012, 489, 391–399. [Google Scholar] [CrossRef] [Green Version]
- Jones, A.R.; Overly, C.C.; Sunkin, S.M. The Allen Brain Atlas: 5 years and beyond. Nat. Rev. Neurosci. 2009, 10, 821–828. [Google Scholar] [CrossRef]
- Martins, D.; Giacomel, A.; Williams, S.C.; Turkheimer, F.; Dipasquale, O.; Veronese, M. Imaging transcriptomics: Convergent cellular, transcriptomic, and molecular neuroimaging signatures in the healthy adult human brain. Cell Rep. 2021, 37, 110173. [Google Scholar] [CrossRef] [PubMed]
- Shen, E.H.; Overly, C.C.; Jones, A.R. The Allen Human Brain Atlas. Trends Neurosci. 2012, 35, 711–714. [Google Scholar] [CrossRef]
- Sporns, O.; Tononi, G.; Kötter, R. The Human Connectome: A Structural Description of the Human Brain. PLoS Comput. Biol. 2005, 1, e42. [Google Scholar] [CrossRef] [PubMed]
- Van Essen, D.C.; Smith, S.M.; Barch, D.M.; Behrens, T.E.J.; Yacoub, E.; Ugurbil, K. The WU-Minn Human Connectome Project: An overview. NeuroImage 2013, 80, 62–79. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Germann, J.; Elias, G.J.B.; Neudorfer, C.; Boutet, A.; Chow, C.T.; Wong, E.H.Y.; Parmar, R.; Gouveia, F.V.; Loh, A.; Giacobbe, P.; et al. Potential optimization of focused ultrasound capsulotomy for obsessive compulsive disorder. Brain 2021, 144, 3529–3540. [Google Scholar] [CrossRef]
- Joutsa, J.; Moussawi, K.; Siddiqi, S.H.; Abdolahi, A.; Drew, W.; Cohen, A.L.; Ross, T.J.; Deshpande, H.U.; Wang, H.Z.; Bruss, J.; et al. Brain lesions disrupting addiction map to a common human brain circuit. Nat. Med. 2022, 28, 1249–1255. [Google Scholar] [CrossRef]
- Li, N.; Baldermann, J.C.; Kibleur, A.; Treu, S.; Akram, H.; Elias, G.J.B.; Boutet, A.; Lozano, A.M.; Al-Fatly, B.; Strange, B.; et al. A unified connectomic target for deep brain stimulation in obsessive-compulsive disorder. Nat. Commun. 2020, 11, 3364. [Google Scholar] [CrossRef]
- Brett, M.; Johnsrude, I.S.; Owen, A.M. The problem of functional localization in the human brain. Nat. Rev. Neurosci. 2002, 3, 243–249. [Google Scholar] [CrossRef]
- Zotero Software. Available online: http://www.zotero.org (accessed on 2 November 2020).
- Covidence. A Software Product for Sorting References for Reviews. 2016. Available online: https://www.covidence.org/ (accessed on 1 August 2022).
- Team, R. Rstudio: Integrated Development for R; Rstudio: Boston, MA, USA, 2020; Available online: http://www.Rstudio.Com (accessed on 9 September 2022).
- R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2022; Available online: https://www.R-project.org/ (accessed on 17 August 2022).
- You are Crossref—Crossref. Available online: https://www.crossref.org/ (accessed on 17 August 2022).
- Alzheimer’s Disease Neuroimaging Initiative (ADNI). Available online: http://adni.loni.usc.edu/ (accessed on 25 July 2021).
- Home | Parkinson’s Progression Markers Initiative. Available online: https://www.ppmi-info.org/ (accessed on 6 September 2022).
- Cox, S.R.; Ritchie, S.J.; Tucker-Drob, E.M.; Liewald, D.C.; Hagenaars, S.P.; Davies, G.; Wardlaw, J.M.; Gale, C.R.; Bastin, M.E.; Deary, I.J. Ageing and brain white matter structure in 3,513 UK Biobank participants. Nat. Commun. 2016, 7, 13629. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pallud, J.; Roux, A.; Trancart, B.; Peeters, S.; Moiraghi, A.; Edjlali, M.; Oppenheim, C.; Varlet, P.; Chrétien, F.; Dhermain, F.; et al. Surgery of Insular Diffuse Gliomas—Part 2. Neurosurgery 2021, 89, 579–590. [Google Scholar] [CrossRef] [PubMed]
- Mansouri, A.; Boutet, A.; Elias, G.; Germann, J.; Yan, H.; Babu, H.; Lozano, A.; Valiante, T.A. Lesion Network Mapping Analysis Identifies Potential Cause of Postoperative Depression in a Case of Cingulate Low-Grade Glioma. World Neurosurg. 2019, 133, 278–282. [Google Scholar] [CrossRef] [PubMed]
- Hart, M.G.; Price, S.J.; Suckling, J. Connectome analysis for pre-operative brain mapping in neurosurgery. Br. J. Neurosurg. 2016, 30, 506–517. [Google Scholar] [CrossRef] [Green Version]
- Latini, F.; Fahlström, M.; Beháňová, A.; Sintorn, I.-M.; Hodik, M.; Staxäng, K.; Ryttlefors, M. The link between gliomas infiltration and white matter architecture investigated with electron microscopy and diffusion tensor imaging. NeuroImage Clin. 2021, 31, 102735. [Google Scholar] [CrossRef]
- Derks, J.; Dirkson, A.R.; Hamer, P.C.D.W.; van Geest, Q.; Hulst, H.E.; Barkhof, F.; Pouwels, P.J.; Geurts, J.J.; Reijneveld, J.C.; Douw, L. Connectomic profile and clinical phenotype in newly diagnosed glioma patients. NeuroImage Clin. 2017, 14, 87–96. [Google Scholar] [CrossRef]
- Fan, X.; Wang, Y.; Wang, K.; Liu, S.; Liu, Y.; Ma, J.; Li, S.; Jiang, T. Anatomical specificity of vascular endothelial growth factor expression in glioblastomas: A voxel-based mapping analysis. Neuroradiology 2015, 58, 69–75. [Google Scholar] [CrossRef] [PubMed]
- Kyeong, S.; Cha, Y.J.; Ahn, S.J.; Suh, S.H.; Son, E.J. Subtypes of breast cancer show different spatial distributions of brain metastases. PLoS ONE 2017, 12, e0188542. [Google Scholar] [CrossRef]
- Liu, T.T.; Achrol, A.S.; Mitchell, L.A.; Du, W.A.; Loya, J.J.; Rodriguez, S.A.; Feroze, A.; Westbroek, E.M.; Yeom, K.W.; Stuart, J.M.; et al. Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas. Am. J. Neuroradiol. 2016, 37, 621–628. [Google Scholar] [CrossRef]
- Wilson, S.M.; Lam, D.; Babiak, M.C.; Perry, D.W.; Shih, T.; Hess, C.P.; Berger, M.S.; Chang, E.F. Transient aphasias after left hemisphere resective surgery. J. Neurosurg. 2015, 123, 581–593. [Google Scholar] [CrossRef] [Green Version]
- Campanella, F.; Shallice, T.; Ius, T.; Fabbro, F.; Skrap, M. Impact of brain tumour location on emotion and personality: A voxel-based lesion–symptom mapping study on mentalization processes. Brain 2014, 137, 2532–2545. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Loit, M.-P.; Rheault, F.; Gayat, E.; Poisson, I.; Froelich, S.; Zhi, N.; Velut, S.; Mandonnet, E. Hotspots of small strokes in glioma surgery: An overlooked risk? Acta Neurochir. 2018, 161, 91–98. [Google Scholar] [CrossRef] [PubMed]
- Rech, F.; Wassermann, D.; Duffau, H. New insights into the neural foundations mediating movement/language interactions gained from intrasurgical direct electrostimulations. Brain Cogn. 2020, 142, 105583. [Google Scholar] [CrossRef] [PubMed]
- Yordanova, Y.N.; Cochereau, J.; Duffau, H.; Herbet, G. Combining resting state functional MRI with intraoperative cortical stimulation to map the mentalizing network. NeuroImage 2018, 186, 628–636. [Google Scholar] [CrossRef]
- Visser, M.; Petr, J.; Müller, D.M.J.; Eijgelaar, R.S.; Hendriks, E.J.; Witte, M.; Barkhof, F.; Van Herk, M.; Mutsaerts, H.J.M.M.; Vrenken, H.; et al. Accurate MR Image Registration to Anatomical Reference Space for Diffuse Glioma. Front. Neurosci. 2020, 14, 585. [Google Scholar] [CrossRef]
- Doyen, S.; Nicholas, P.; Poologaindran, A.; Crawford, L.; Young, I.M.; Romero-Garcia, R.; Sughrue, M.E. Connectivity-based parcellation of normal and anatomically distorted human cerebral cortex. Hum. Brain Mapp. 2021, 43, 1358–1369. [Google Scholar] [CrossRef]
- Tang, Z.; Wu, Y.; Fan, Y. Groupwise registration of MR brain images with tumors. Phys. Med. Biol. 2017, 62, 6853–6868. [Google Scholar] [CrossRef]
- Tang, Z.; Ahmad, S.; Yap, P.-T.; Shen, D. Multi-Atlas Segmentation of MR Tumor Brain Images Using Low-Rank Based Image Recovery. IEEE Trans. Med. Imaging 2018, 37, 2224–2235. [Google Scholar] [CrossRef]
- O’Donnell, L.J.; Suter, Y.; Rigolo, L.; Kahali, P.; Zhang, F.; Norton, I.; Albi, A.; Olubiyi, O.; Meola, A.; Essayed, W.I.; et al. Automated white matter fiber tract identification in patients with brain tumors. NeuroImage Clin. 2017, 13, 138–153. [Google Scholar] [CrossRef]
- Zhang, W.; Olivi, A.; Hertig, S.J.; van Zijl, P.; Mori, S. Automated fiber tracking of human brain white matter using diffusion tensor imaging. NeuroImage 2008, 42, 771–777. [Google Scholar] [CrossRef] [Green Version]
- Guye, M.; Parker, G.J.; Symms, M.; Boulby, P.; Wheeler-Kingshott, C.A.; Salek-Haddadi, A.; Barker, G.J.; Duncan, J.S. Combined functional MRI and tractography to demonstrate the connectivity of the human primary motor cortex in vivo. Neuroimage 2003, 19, 1349–1360. [Google Scholar] [CrossRef] [PubMed]
- Akkus, Z.; Sedlar, J.; Coufalova, L.; Korfiatis, P.; Kline, T.L.; Warner, J.D.; Agrawal, J.; Erickson, B.J. Semi-automated segmentation of pre-operative low grade gliomas in magnetic resonance imaging. Cancer Imaging 2015, 15, 12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Roniotis, A.; Marias, K.; Sakkalis, V.; Manikis, G.C.; Zervakis, M. Simulating Radiotherapy Effect in High-Grade Glioma by Using Diffusive Modeling and Brain Atlases. J. Biomed. Biotechnol. 2012, 2012, 715812. [Google Scholar] [CrossRef] [PubMed]
Example Analysis Tool | Description | Source |
---|---|---|
Functional connectome analysis | Using functional connectivity maps created using fMRI data from a large cohort of healthy individuals (Brain Genomics Superstructure Project dataset; http://neuroinformatics.harvard.edu/gsp; accessed on 1 August 2022) to identify functional brain networks. | http://neuroinformatics.harvard.edu/gsp; accessed on 1 August 2022 https://www.lead-dbs.org/; accessed on 1 August 2022 |
Structural connectome analysis | Using structural maps constructed using dMRI data from large cohorts of healthy individuals (Human Connectome Project; https://www.humanconnectome.org/; accessed on 1 August 2022) to identify structural brain networks. | https://www.humanconnectome.org/; accessed on 1 August 2022 https://www.lead-dbs.org/; accessed on 1 August 2022 |
Spatial transcriptome analysis | Using 3D spatial maps of gene expression to identify | https://human.brain-map.org/; accessed on 1 August 2022 https://doi.org/10.7554/eLife.72129; accessed on 1 August 2022 https://abagen.readthedocs.io/en/stable/; accessed on 1 August 2022 |
High resolution histological atlases | 3D histological brain atlases and architectonic maps (cytoarchitecture and molecular) | https://julich-brain-atlas.de/atlas; accessed on 1 August 2022 https://bigbrainproject.org/; accessed on 1 August 2022 |
Hypothalamic atlas | Detailed 3-D atlas of the human hypothalamic regions | https://doi.org/10.5281/zenodo.3724192; accessed on 1 August 2022 https://zenodo.org/record/3724192; accessed on 1 August 2022 |
Neurosynth maps | Maps of brain areas associated with the function/process of interest, generated using meta analysis of reported fMRI findings | https://neurosynth.org/; accessed on 1 August 2022 |
Receptor maps | Maps of neurotransmitters generated from large PET imaging datasets | https://doi.org/10.1038/s41593-022-01186-3; accessed on 1 August 2022 https://github.com/netneurolab/hansen_gene-receptor; accessed on 1 August 2022 |
Cortical expansion during development and evolution | Map of estimated brain expansion during development and evolution | https://doi.org/10.1073/pnas.1001229107; accessed on 1 August 2022 https://doi.org/10.1038/s41592-022-01625-w; accessed on 1 August 2022 https://github.com/netneurolab/neuromaps; accessed on 1 August 2022 |
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Germann, J.; Yang, A.; Chow, C.T.; Santyr, B.; Samuel, N.; Vetkas, A.; Sarica, C.; Elias, G.J.B.; Voisin, M.R.; Kucharczyk, W.; et al. Review of Template-Based Neuroimaging Tools in Neuro-Oncology: Novel Insights. Onco 2023, 3, 1-12. https://doi.org/10.3390/onco3010001
Germann J, Yang A, Chow CT, Santyr B, Samuel N, Vetkas A, Sarica C, Elias GJB, Voisin MR, Kucharczyk W, et al. Review of Template-Based Neuroimaging Tools in Neuro-Oncology: Novel Insights. Onco. 2023; 3(1):1-12. https://doi.org/10.3390/onco3010001
Chicago/Turabian StyleGermann, Jürgen, Andrew Yang, Clement T. Chow, Brendan Santyr, Nardin Samuel, Artur Vetkas, Can Sarica, Gavin J. B. Elias, Mathew R. Voisin, Walter Kucharczyk, and et al. 2023. "Review of Template-Based Neuroimaging Tools in Neuro-Oncology: Novel Insights" Onco 3, no. 1: 1-12. https://doi.org/10.3390/onco3010001
APA StyleGermann, J., Yang, A., Chow, C. T., Santyr, B., Samuel, N., Vetkas, A., Sarica, C., Elias, G. J. B., Voisin, M. R., Kucharczyk, W., Zadeh, G., Lozano, A. M., & Boutet, A. (2023). Review of Template-Based Neuroimaging Tools in Neuro-Oncology: Novel Insights. Onco, 3(1), 1-12. https://doi.org/10.3390/onco3010001