Ecog GUI is a Python module to localize intracranial electrodes from MRI.
It interactively fits a priori defined grids, strips or rigid array of electrodes to the MRI with a Graphical User Interface.
Its main advantages as compared to current alternatives are:
- it provides the best fits in real time, and can thus help you adjust your locations interactively.
- it can fit curved surfaces, including non-convex ones, but remains realistic thanks to a rigidity constrain.
This is currently an alpha version.
Click on the following examples to run the tutorial and results preview in your browser.
examples/model_displacement.ipynbhow the 2D grid/strips are fitted with a rotation and translation to match the 3D locations.examples/model_surface.ipynb: how the 2D grid/strips are fitted with a 2nd order polynomial with a constrain on the electrodes local distances, as we know the grid can be flexible but is not elastic.examples/gui_mri_ecog.ipynb: try to fit the grid this patient brain. It should take no more than five minutes.
Clone this repository and install using setup.py:
python setup.py develop --user
The required dependencies to use the software are:
- Python >= 2.7
- setuptools
- Numpy >= 1.6.1
- SciPy >= 0.9
- Scikit-learn >= 0.17
- Nibabel >= 1.1.0
- Matplotlib >= 1.5.1