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Welcome to iElectrodes wiki!

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News section:

We just released a new version of iElectrodes v_1.020. This new version includes major upgrades in the localization and projection algorithms.
We are happy to introduce:
1) GridFit to localize CT electrode artifacts using a model-based approach.
2) CEPA a Combined Electrode Projection Algorithm that takes the best of spring-mesh-like models and orthogonal projections. The result is nicely projected grids that expand with distance (as expected by basic physics) plus conserved interelectrode distance.
Check our last paper to know more about these new algorithms Blenkmann et al., 2024 in Journal of Neuroscience Methods.

We have also recently introduced a new grid/strip simulation algorithm, Blenkmann et al., 2022 in Frontiens Neuroinformatics.
The new paper presents the CT artifact and noise modeling algorithms available using command-line scripts.

The wiki pages are being updated to represent the new features. Thanks for your patience.

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What is iElectrodes?

iElectrodes is an open-source Matlab toolbox for intracranial electrode (SEEG and ECoG) localization and labeling.
Information about the methods behind iElectrodes can be found in our paper Blenkmann et al., 2017 in Frontiens Neuroinformatics.
Information about how to use the toolbox is in the Help Guide below.

Want to stay updated? Subscribe to iElectrodes Mailing list to be notified of the following releases. Remember that iElectrodes is still under development. Some bugs may appear, so please report them! We want to make a useful toolbox, so your comments are welcome to improve it.

About us: The iElectrodes toolbox is developed and maintained by Alejandro O. Blenkmann

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Last version vs. Overnight?

Download the last stable version (v1.020) of iElectrodes from the Files tab.
Under the tab Code, you will find the overnight version with the newest features of iElectrodes. However, there might be some bugs in this version. We would appreciate you contributing to this project by using the overnight version and reporting bugs.

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Note: We recommend using Matlab 2016a or later to avoid some graphical errors in the Matlab graphics engine.

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Last stable version:
May 2023 v1.020
- GridFit algorithm for localizing electrodes´ CT artifacts
- CEPA for projecting grids to the Smooth Cortical Envelope (SCE)
- Minor bugs corrected

Check previous for previous [Updates]

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Help Guide - Step by step how to use iElectrodes

[Installation] - Here, you will find information on how to install iElectrodes.

[Pre-processing] - Pre-processing steps before loading images.

[Some Freesurfer notes] - Pre-processing notes for the Freesurfer pipeline

[Load images] - Loading MRI and CT images.

[2D - 3D visualization] - 2D and 3D visualization options

[Localization and labeling of intracranial electrodes] - Localize depth and grid electrodes and label them.
Project grids to the cortical surface. Watch tutorial videos!

[Planning] - Depth electrodes planning. Watch the tutorial video!

[Planning coordinates and implantation surgery] - Planned electrode coordinates can be compared to final electrode localizations after implantation.

[Manual Indexing] - How to manually fix the automatic electrode indexing if it fails.

[The electrodes structure] - Information regarding the data structure electrodes that can be exported after the localization procedure

[Cite Us - References] - List of publications and citation references.

[Updates] - List of updates

iElectrodes toolbox is FOR RESEARCH PURPOSES ONLY.
This software is for research purposes only and has not been approved for clinical use.

Suppose you publish results whose generation used this toolbox. In that case, we will be grateful if you provide attribution to the authors of the software by referencing the appropriate papers, as outlined in the [Cite Us] page.