Modular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
02
12
2022
accepted:
15
06
2023
medline:
10
7
2023
pubmed:
7
7
2023
entrez:
7
7
2023
Statut:
epublish
Résumé
Implantation of electrodes in the brain has been used as a clinical tool for decades to stimulate and record brain activity. As this method increasingly becomes the standard of care for several disorders and diseases, there is a growing need to quickly and accurately localize the electrodes once they are placed within the brain. We share here a protocol pipeline for localizing electrodes implanted in the brain, which we have applied to more than 260 patients, that is accessible to multiple skill levels and modular in execution. This pipeline uses multiple software packages to prioritize flexibility by permitting multiple different parallel outputs while minimizing the number of steps for each output. These outputs include co-registered imaging, electrode coordinates, 2D and 3D visualizations of the implants, automatic surface and volumetric localizations of the brain regions per electrode, and anonymization and data sharing tools. We demonstrate here some of the pipeline's visualizations and automatic localization algorithms which we have applied to determine appropriate stimulation targets, to conduct seizure dynamics analysis, and to localize neural activity from cognitive tasks in previous studies. Further, the output facilitates the extraction of information such as the probability of grey matter intersection or the nearest anatomic structure per electrode contact across all data sets that go through the pipeline. We expect that this pipeline will be a useful framework for researchers and clinicians alike to localize implanted electrodes in the human brain.
Identifiants
pubmed: 37418486
doi: 10.1371/journal.pone.0287921
pii: PONE-D-22-33193
pmc: PMC10328232
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0287921Subventions
Organisme : NINDS NIH HHS
ID : R01 NS079533
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS062092
Pays : United States
Organisme : NINDS NIH HHS
ID : K24 NS088568
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS072023
Pays : United States
Organisme : NINDS NIH HHS
ID : R56 NS062092
Pays : United States
Organisme : NIMH NIH HHS
ID : R21 MH127009
Pays : United States
Informations de copyright
Copyright: © 2023 Soper et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Front Neurosci. 2021 Dec 09;15:769872
pubmed: 34955721
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Front Neurol. 2020 Sep 17;11:553885
pubmed: 33041993
Neurology. 2002 Mar 12;58(5):695-701
pubmed: 11889230
Brain. 2019 Dec 1;142(12):3892-3905
pubmed: 31599323
Nat Biomed Eng. 2023 Apr;7(4):576-588
pubmed: 34725508
Neuron. 2002 Jan 31;33(3):341-55
pubmed: 11832223
Neuroimage. 2022 Jul 1;254:119165
pubmed: 35378289
Neuroimage. 2021 Aug 15;237:118094
pubmed: 33940142
Front Hum Neurosci. 2011 Aug 03;5:74
pubmed: 21886615
Neuroimage. 2022 Oct 15;260:119438
pubmed: 35792291
Brain Stimul. 2022 May-Jun;15(3):554-565
pubmed: 35292403
Nat Protoc. 2018 Jul;13(7):1699-1723
pubmed: 29988107
Brain. 2007 Dec;130(Pt 12):3169-83
pubmed: 17855377
Neuroimage. 2012 Feb 15;59(4):3563-70
pubmed: 22155045
Neuroimage. 2021 Dec 1;244:118608
pubmed: 34560270
Neuroimage. 2006 Apr 1;30(2):436-43
pubmed: 16300968
Neurobiol Dis. 2022 Apr;165:105645
pubmed: 35104646
JAMA Neurol. 2019 Sep 01;76(9):1070-1078
pubmed: 31180505
IEEE Trans Med Imaging. 1998 Feb;17(1):87-97
pubmed: 9617910
Annu Int Conf IEEE Eng Med Biol Soc. 2020 Jul;2020:3586-3589
pubmed: 33018778
Comput Intell Neurosci. 2011;2011:879716
pubmed: 21584256
Magn Reson Imaging. 2012 Nov;30(9):1323-41
pubmed: 22770690
J Neurosci Methods. 2018 Jun 1;303:7-15
pubmed: 29605667
Front Neuroeng. 2014 Jun 12;7:16
pubmed: 24971060
Front Neuroinform. 2018 Jul 06;12:40
pubmed: 30034332
Neuroimage. 2020 Dec;223:117314
pubmed: 32882382
Biol Psychiatry. 2022 Aug 1;92(3):246-251
pubmed: 35063186
Brain Stimul. 2019 Jul - Aug;12(4):877-892
pubmed: 30904423
Front Neuroinform. 2017 Mar 02;11:14
pubmed: 28303098
Nat Med. 2021 Oct;27(10):1696-1700
pubmed: 34608328
Hum Brain Mapp. 1999;8(4):272-84
pubmed: 10619420
World Neurosurg. 2015 Sep;84(3):719-26
pubmed: 25940211
Nat Med. 2021 Dec;27(12):2154-2164
pubmed: 34887577
Comput Intell Neurosci. 2011;2011:156869
pubmed: 21253357
Clin Neurophysiol. 2020 Aug;131(8):1782-1797
pubmed: 32512346
Neuroimage. 2012 Jul 16;61(4):1402-18
pubmed: 22430496
Neuroimage. 2002 Jan;15(1):273-89
pubmed: 11771995
Front Neurol. 2020 Oct 15;11:595454
pubmed: 33178129
Sci Data. 2023 Feb 9;10(1):83
pubmed: 36759619
Front Neuroinform. 2011 Oct 14;5:23
pubmed: 22016733
Nat Commun. 2019 Apr 4;10(1):1536
pubmed: 30948727
Epilepsia. 2022 Feb;63(2):483-496
pubmed: 34919741
Neuroimage. 2021 Dec 15;245:118706
pubmed: 34780916
Exp Neurol. 2017 Jan;287(Pt 4):461-472
pubmed: 27485972
IEEE Trans Med Imaging. 2007 Apr;26(4):518-29
pubmed: 17427739
Neuroimage. 1999 Feb;9(2):179-94
pubmed: 9931268
Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11050-5
pubmed: 10984517
Brain. 2018 Apr 1;141(4):1130-1144
pubmed: 29506200
Epilepsia. 2021 Apr;62(4):947-959
pubmed: 33634855
Nat Med. 2021 Feb;27(2):229-231
pubmed: 33462446
Neuroimage. 2006 Jul 1;31(3):968-80
pubmed: 16530430
Neuroimage. 2012 Oct 15;63(1):157-165
pubmed: 22759995
J Neurosci Methods. 2017 Apr 1;281:40-48
pubmed: 28192130
Sci Data. 2019 Jun 25;6(1):102
pubmed: 31239438
Cereb Cortex. 2004 Jan;14(1):11-22
pubmed: 14654453
J Neurosci Methods. 2010 Jan 15;185(2):293-8
pubmed: 19836416
Neuroinformatics. 2011 Dec;9(4):371-80
pubmed: 21360205
Neuroimage. 2006 Aug 1;32(1):180-94
pubmed: 16651008
Clin Neurophysiol Pract. 2018 Jun 23;3:120-121
pubmed: 30215021
Neuroinformatics. 2010 Oct;8(3):171-82
pubmed: 20582489
Neuroimage. 2011 Jul 1;57(1):19-21
pubmed: 21376812
Neuroscientist. 2012 Aug;18(4):360-72
pubmed: 22235060
Neuroimage. 2010 Dec;53(4):1181-96
pubmed: 20637289
IEEE Trans Med Imaging. 2001 Jan;20(1):70-80
pubmed: 11293693
Front Neuroinform. 2012 Aug 28;6:23
pubmed: 22973224
Front Psychiatry. 2021 Feb 24;12:617997
pubmed: 33716819
Cereb Cortex. 2004 Jul;14(7):721-30
pubmed: 15054051
Annu Int Conf IEEE Eng Med Biol Soc. 2010;2010:2057-60
pubmed: 21096151
Arch Gen Psychiatry. 2003 Sep;60(9):878-88
pubmed: 12963669
Neuroimage. 2015 Feb 15;107:127-135
pubmed: 25498389
Neuroimage. 2004;23 Suppl 1:S69-84
pubmed: 15501102
Int J Comput Assist Radiol Surg. 2017 Oct;12(10):1829-1837
pubmed: 27915398
Brain Stimul. 2022 Mar-Apr;15(2):491-508
pubmed: 35247646
Neuroimage. 1999 Feb;9(2):195-207
pubmed: 9931269
Nat Commun. 2023 Mar 29;14(1):1748
pubmed: 36991011
J Neural Eng. 2019 Aug 16;16(5):056015
pubmed: 31419211
Neuroimage. 2004 Jul;22(3):1060-75
pubmed: 15219578