Simeon Wong
Ibrahim Lab @ SickKids
Automatically mark electrode contacts in post-insertion CT imaging, roughly cluster into electrodes, then warp coordinates into standard MNI space.
- requires FMRIB Software Library (FSL)
- requires X Windows System with OpenGL (eg. direct desktop access or VirtualGL headless)
pip install git+https://github.com/gmilab/seeglocseegloc_coreg /path/to/ct.nii.gz /path/to/mri.nii.gz /path/to/subject/coreg_output_dir
seegloc_autolabel /path/to/subject/coreg_output_dirIf this code has been useful in your work, please cite:
Wong SM, Arski ON, Ibrahim GM. An automated algorithm for stereoelectroencephalography electrode localization and labelling. Seizure: European Journal of Epilepsy. 2024;117:293-297. doi:10.1016/j.seizure.2024.04.002
| ename | x | y | z | aal | entry |
|---|---|---|---|---|---|
| A-01 | -43.3236 | 2.77232 | 40.8664 | Precentral_L | FC3 |
| A-02 | -38.8153 | 2.01561 | 38.612 | Precentral_L | FC3 |
| A-03 | -34.0798 | 1.52495 | 36.5061 | Precentral_L | FC3 |
| A-04 | -28.3241 | 0.982843 | 34.7693 | Frontal_Mid_2_L | FC3 |
| A-05 | -19.7692 | -1.11625 | 33.8938 | Cingulate_Mid_L | FC3 |
Automatic electrode segmentation from CT may not always work in some cases where individual electrodes are not easily identified (eg. electrode is so bright there is no space between electrode contacts).
In this case:
- Using CT viewing software (eg.
fsleyes), note the CT scanner-space coordinates in mm of:- The tip (deepest contact) of the electrode trajectory
- Any other point along the trajectory
- Run the
seegloc_extrapolatecommand:
seegloc_extrapolate [spacing in mm] [number of contacts] \
[tip_x] [tip_y] [tip_z] \
[other_x] [other_y] [other_z] \
--coreg /path/to/subject/coreg_output_dir- scipy label / regionprops for contact identification
- custom code for electrode clustering
- fsl flirt (linear coregistration) of CT <=> Subject MRI
- fsl fnirt (non-linear coregistration) of Subject MRI <=> MNI152 template