GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation | Neuroinformatics
Skip to main content
Springer Nature Link
Log in

GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation

  • Original Article
  • Published:
Neuroinformatics Aims and scope Submit manuscript

Abstract

NonInvasive Brain Stimulation (NIBS) is a potential therapeutic tool with growing interest, but neuronavigation-guided software and tools available for the target determination are mostly either expensive or closed proprietary applications. To address these limitations, we propose GeodesicSlicer, a customizable, free, and open-source NIBS therapy research toolkit. GeodesicSlicer is implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. GeodesicSlicer uses cortical stimulation target from either functional or anatomical images to provide functionality specifically designed for NIBS therapy research. The provided algorithms are tested and they are accessible through a convenient graphical user interface. Modules have been created for NIBS target determination according to the position of the electrodes in the 10–20 system electroencephalogram and calculating correction factors to adjust the repetitive Transcranial Magnetic Stimulation (rTMS) dose for the treatment. Two illustrative examples are processing with the module. This new open-source software has been developed for NIBS therapy: GeodesicSlicer is an alternative for laboratories that do not have access to neuronavigation system. The triangulation-based MRI-guided method presented here provides a reproducible and inexpensive way to position the TMS coil that may be used without the use of a neuronavigation system.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Japan)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Andoh, J., Riviere, D., Mangin, J. F., Artiges, E., Cointepas, Y., Grevent, D., Paillère-Martinot, M. L., Martinot, J. L., & Cachia, A. (2009). A triangulation-based magnetic resonance image-guided method for transcranial magnetic stimulation coil positioning. Brain Stimulation, 2(3), 123–131. https://doi.org/10.1016/j.brs.2008.10.002.

  • Beam, W., Borckardt, J. J., Reeves, S. T., & George, M. S. (2009). An efficient and accurate new method for locating the F3 position for prefrontal TMS applications. Brain Stimulation, 2(1), 50–54. https://doi.org/10.1016/j.brs.2008.09.006.

  • Bland, J. M., & Altman, D. G. (1999). Measuring agreement in method comparison studies. Statistical Methods in Medical Research, 8(2), 135–160.

    Article  CAS  Google Scholar 

  • Dayan, E., Thompson, R. M., Buch, E. R., & Cohen, L. G. (2016). 3D-printed head models for navigated non-invasive brain stimulation. Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology, 127(10), 3341–3342. https://doi.org/10.1016/j.clinph.2016.08.011.

  • De Witte, S., Klooster, D., Dedoncker, J., Duprat, R., Remue, J., & Baeken, C. (2018). Left prefrontal neuronavigated electrode localization in tDCS: 10–20 EEG system versus MRI-guided neuronavigation. Psychiatry Research: Neuroimaging, 274, 1–6. https://doi.org/10.1016/j.pscychresns.2018.02.001.

  • Dijkstra, E. W. (1959). A note on two problems in connexion with graphs. Numerische Mathematik, 1(1), 269–271. https://doi.org/10.1007/BF01386390.

  • Dollfus, S., Jaafari, N., Guillin, O., Trojak, B., Plaze, M., Saba, G., Nauczyciel, C., Montagne Larmurier, A., Chastan, N., Meille, V., Krebs, M. O., Ayache, S. S., Lefaucheur, J. P., Razafimandimby, A., Leroux, E., Morello, R., Marie Batail, J., Brazo, P., Lafay, N., Wassouf, I., Harika-Germaneau, G., Guillevin, R., Guillevin, C., Gerardin, E., Rotharmel, M., Crépon, B., Gaillard, R., Delmas, C., Fouldrin, G., Laurent, G., Nathou, C., & Etard, O. (2018). High-frequency Neuronavigated rTMS in auditory verbal hallucinations: A pilot double-blind controlled study in patients with schizophrenia. Schizophrenia Bulletin, 44(3), 505–514. https://doi.org/10.1093/schbul/sbx127.

    Article  PubMed  Google Scholar 

  • Fox, M. D., Liu, H., & Pascual-Leone, A. (2013). Identification of reproducible individualized targets for treatment of depression with TMS based on intrinsic connectivity. NeuroImage, 66, 151–160. https://doi.org/10.1016/j.neuroimage.2012.10.082.

    Article  PubMed  Google Scholar 

  • Herbsman, T., & Nahas, Z. (2011). Anatomically based targeting of prefrontal cortex for rTMS. Brain Stimulation, 4(4), 300–302. https://doi.org/10.1016/j.brs.2011.01.004.

    Article  PubMed  PubMed Central  Google Scholar 

  • Herwig, U., Padberg, F., Unger, J., Spitzer, M., & Schönfeldt-Lecuona, C. (2001). Transcranial magnetic stimulation in therapy studies: Examination of the reliability of “standard” coil positioning by neuronavigation. Biological Psychiatry, 50(1), 58–61.

    Article  CAS  Google Scholar 

  • Herwig, U., Satrapi, P., & Schönfeldt-Lecuona, C. (2003). Using the international 10-20 EEG system for positioning of transcranial magnetic stimulation. Brain Topography, 16(2), 95–99.

    Article  Google Scholar 

  • Hoffman, R. E., Boutros, N. N., Berman, R. M., Roessler, E., Belger, A., Krystal, J. H., & Charney, D. S. (1999). Transcranial magnetic stimulation of left temporoparietal cortex in three patients reporting hallucinated “voices”. Biological Psychiatry, 46(1), 130–132.

    Article  CAS  Google Scholar 

  • Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and right homologous sites to curtail “voices:” a randomized trial. Biological Psychiatry, 73(10), 1008–1014. https://doi.org/10.1016/j.biopsych.2013.01.016.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371–375.

    Google Scholar 

  • Klem, G. H., Lüders, H. O., Jasper, H. H., & Elger, C. (1999). The ten-twenty electrode system of the international federation. The International Federation of Clinical Neurophysiology. Electroencephalography and Clinical Neurophysiology. Supplement, 52, 3–6.

    CAS  PubMed  Google Scholar 

  • Kraus, D., & Gharabaghi, A. (2015). Projecting navigated TMS sites on the Gyral anatomy decreases inter-subject variability of cortical motor maps. Brain Stimulation, 8(4), 831–837. https://doi.org/10.1016/j.brs.2015.03.006.

    Article  PubMed  Google Scholar 

  • Lahti, A. C. (2016). Making Progress toward individualized medicine in the treatment of psychosis. The American Journal of Psychiatry, 173(1), 5–7. https://doi.org/10.1176/appi.ajp.2016.15101320.

    Article  PubMed  Google Scholar 

  • McGirr, A., Van den Eynde, F., Tovar-Perdomo, S., Fleck, M. P. A., & Berlim, M. T. (2015). Effectiveness and acceptability of accelerated repetitive transcranial magnetic stimulation (rTMS) for treatment-resistant major depressive disorder: An open label trial. Journal of Affective Disorders, 173, 216–220. https://doi.org/10.1016/j.jad.2014.10.068.

    Article  PubMed  Google Scholar 

  • Niyazov, D. M., Butler, A. J., Kadah, Y. M., Epstein, C. M., & Hu, X. P. (2005). Functional magnetic resonance imaging and transcranial magnetic stimulation: Effects of motor imagery, movement and coil orientation. Clinical Neurophysiology, 116(7), 1601–1610. https://doi.org/10.1016/j.clinph.2005.02.028.

    Article  CAS  PubMed  Google Scholar 

  • Pieper, S., Lorensen, B., Schroeder, W., & Kikinis, R. (2006). The NA-MIC kit: ITK, VTK, pipelines, grids and 3D slicer as an open platform for the medical image computing community. In 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2006. (pp. 698–701). Presented at the 3rd IEEE international symposium on biomedical imaging: Nano to macro, 2006. https://doi.org/10.1109/ISBI.2006.1625012.

  • Pinter, C., Lasso, A., Wang, A., Jaffray, D., & Fichtinger, G. (2012). SlicerRT: Radiation therapy research toolkit for 3D slicer. Medical Physics, 39(10), 6332–6338. https://doi.org/10.1118/1.4754659.

    Article  PubMed  Google Scholar 

  • Rodseth, J., WashaBaugh, E. P., & Krishnan, C. (2017). A novel low-cost approach for navigated Transcranial magnetic stimulation. Restorative Neurology and Neuroscience, 35(6), 601–609. https://doi.org/10.3233/RNN-170751.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rossi, S., Hallett, M., Rossini, P. M., Pascual-Leone, A., & Safety of TMS Consensus Group. (2009). Safety, ethical considerations, and application guidelines for the use of transcranial magnetic stimulation in clinical practice and research. Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology, 120(12), 2008–2039. https://doi.org/10.1016/j.clinph.2009.08.016.

    Article  Google Scholar 

  • Sommer, I. E. C., de Weijer, A. D., Daalman, K., Neggers, S. F., Somers, M., Kahn, R. S., et al. (2007). Can fMRI-guidance improve the efficacy of rTMS treatment for auditory verbal hallucinations? Schizophrenia Research, 93(1–3), 406–408. https://doi.org/10.1016/j.schres.2007.03.020.

    Article  CAS  PubMed  Google Scholar 

  • Sommer, I. E., Kleijer, H., & Hugdahl, K. (2018). Toward personalized treatment of hallucinations. Current Opinion in Psychiatry, 31(3), 237–245. https://doi.org/10.1097/YCO.0000000000000416.

    Article  PubMed  Google Scholar 

  • Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617–1625. https://doi.org/10.1016/j.clinph.2007.04.004.

    Article  PubMed  Google Scholar 

  • Summers, P. M., & Hanlon, C. A. (2017). BrainRuler-a free, open-access tool for calculating scalp to cortex distance. Brain Stimulation, 10(5), 1009–1010. https://doi.org/10.1016/j.brs.2017.03.003.

    Article  PubMed  PubMed Central  Google Scholar 

  • Trojak, B., Meille, V., Chauvet-Gelinier, J.-C., & Bonin, B. (2012). Does the intensity of transcranial magnetic stimulation need to be adjusted to scalp-cortex distance? The Journal of Neuropsychiatry and Clinical Neurosciences, 24(2), E13. https://doi.org/10.1176/appi.neuropsych.11050114.

    Article  PubMed  Google Scholar 

  • Vaghefi, E., Cai, P., Fang, F., Byblow, W. D., Stinear, C. M., & Thompson, B. (2015). MRI guided brain stimulation without the use of a Neuronavigation system. BioMed Research International, 2015, 647510. https://doi.org/10.1155/2015/647510.

    Article  PubMed  PubMed Central  Google Scholar 

  • Washabaugh, E. P., & Krishnan, C. (2016). A low-cost system for coil tracking during transcranial magnetic stimulation. Restorative Neurology and Neuroscience, 34(2), 337–346. https://doi.org/10.3233/RNN-150609.

    Article  PubMed  PubMed Central  Google Scholar 

  • Xiao, X., Zhu, H., Liu, W.-J., Yu, X.-T., Duan, L., Li, Z., & Zhu, C.-Z. (2017). Semi-automatic 10/20 identification method for MRI-free probe placement in Transcranial brain mapping techniques. Frontiers in Neuroscience, 11, 4. https://doi.org/10.3389/fnins.2017.00004.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yousry, T. A., Schmid, U. D., Alkadhi, H., Schmidt, D., Peraud, A., Buettner, A., & Winkler, P. (1997). Localization of the motor hand area to a knob on the precentral gyrus. A new landmark. Brain: A Journal of Neurology, 120(Pt 1), 141–157.

    Article  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Drs A. Lasso and K. Yoshimi as well as A. Nourry for their valuable help in 3D Slicer and VTK library, and William P. Armstrong for the English rereading.

Funding Source

This work was supported by the French Health Ministry (Programme Hospitalier de Recherche Clinique), the Fondation Fondamentale, the Association Perceneige, the Region Normandie and the University Caen Normandie.

Author information

Authors and Affiliations

  1. Normandie Univ, UNICAEN, ISTS EA 7466, GIP CYCERON, F-14000, Caen, France

    F. Briend, E. Leroux, C. Nathou, S. Dollfus & O. Etard

  2. CHU de Caen, Service de Psychiatrie adulte, Centre Esquirol, 14000, Caen, France

    C. Nathou & S. Dollfus

  3. Normandie Univ, UNICAEN, CNRS, CHU de Caen, UMS 3408, GIP Cyceron, 14000, Caen, France

    N. Delcroix

  4. Service d’Explorations Fonctionnelles du Système Nerveux, CHU de Caen, 14000, Caen, France

    O. Etard

Authors
  1. F. Briend
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E. Leroux
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C. Nathou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. N. Delcroix
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. S. Dollfus
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. O. Etard
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to F. Briend.

Ethics declarations

Conflict of Interest

The authors have no conflict of interest to declare.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Briend, F., Leroux, E., Nathou, C. et al. GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinform 18, 509–516 (2020). https://doi.org/10.1007/s12021-020-09457-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12021-020-09457-9

Keywords

Search

Navigation