Localize electrodes with CiCLONE
A full walkthrough for turning a patient's implantation imaging into standardized, anatomically-labelled electrode coordinates with CiCLONE - from raw scans to BIDS-ready output.
You'll coregister the post-implantation CT to the pre-implantation MRI, reconstruct the anatomy, localize each electrode contact, transform everything into standard (MNI) space with anatomical labels, and export BIDS-compatible results.
What CiCLONE does
CiCLONE - Clinical imaging Coregistration for Localisation Of Neuro-Electrodes - is an automated pipeline that turns a patient's implantation scans into standardized, anatomically-labelled electrode coordinates. It automates work that is otherwise slow and manual, cutting localization from hours to minutes while improving consistency. It integrates with 3D Slicer and produces BIDS-compatible outputs that drop straight into the rest of your iEEG pipeline.
Follow the demo series
CiCLONE is demonstrated in an EBRAINS eight-part video series that walks through the pipeline screen by screen. Work through the steps below alongside it - each stage here maps to a stage in the series.
Open the CiCLONE demo playlist on YouTube →
What you'll need
SEEG localization uses two images per patient:
- A pre-implantation MRI - the anatomical reference.
- A post-implantation CT - where the implanted electrodes are visible.
Have both uploaded to your workspace, and a session running with CiCLONE available (add it from the Applications catalogue if needed).
The localization workflow
The pipeline runs in eight stages. Exact commands and screens are shown in the video series - the steps below explain what each stage does and what to check.
Reconstruct the anatomy
From the pre-implantation MRI, generate the cortical surface reconstruction and segmentation (FreeSurfer-based). This is the anatomical reference everything else is placed into.
Coregister CT to MRI
Align the post-implantation CT to the MRI using a rigid-body registration, so the electrodes sit correctly in the patient's own anatomy. Check the alignment visually - the skull outlines of CT and MRI should match.
Normalize to standard space
Transform the MRI to a standard template (MNI / ICBM152) so coordinates are comparable across patients and studies.
Localize the contacts
Detect and cluster the electrode contacts on the CT automatically, numbering them along each electrode's trajectory.
Handle obscured contacts
Where imaging artifact hides contacts, localize them semi-automatically: annotate the most distal contact and a second point along the trajectory, and the pipeline infers the rest.
Transform & label
Map every contact into MNI coordinates and label it with an anatomical atlas (for example AAL), so each contact carries a brain-region label.
Quality-control
Review the 2D and 3D visualizations at the intermediate stages and for the final result, to catch registration or localization errors before you rely on the coordinates.
Export
Write out the localization as BIDS-compatible electrode coordinates and labels, ready for analysis.
What you get
The result is a standardized, anatomically-labelled set of MNI coordinates for every electrode contact, in BIDS-compatible form - ready for analysis and for aggregation across patients and studies.
Where to go next
With your electrodes localized, Compute an epileptogenicity map is the natural next analysis - or browse the Applications catalogue for the rest of the tooling.