biostudies-literatureSoper DJTiny Blue Dot FoundationNIMH NIH HHSMassachusetts General Hospital Executive Committee on ResearchNINDS NIH HHSNational Institute of Mental HealthU.S. Army Research Office and Defense Advanced Research Projects AgencyNIHe0287921https://www.ebi.ac.uk/biostudies/studies/S-EPMC10328232biostudies-literatureUnknown18(7)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 visualizatioPloS oneModular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes.PMC103282321 R21 MH127009-01A11K24NS088568R01 NS062092R01-NS072023W81XWH-22-1-0315R01- NS062092R01 NS072023R01 NS079533K24 NS088568R56 NS062092R01-NS079533R21 MH127009Reich DRoss ASoper DJCash SSBasu IPeled NPaulk ACSalami PfalseModular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes.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 visualizatio2023-01-01T00:00:00Z20232025-07-04T03:05:55.74Z2025-04-20T03:43:47.304ZS-EPMC103282323741848610.1371/journal.pone.0287921