SEECOG
3D visualization tool
Hosted at seecogviewer.github.io
This tool is developed by Noah Markowitz and Dr. Stephan Bickel of The Human Brain Mapping Laboratory at NorthShore University Hospital.
Creating SEECOG Data and Directory
Before starting, make sure:
- Freesurfer is installed on your computer
- You have a python environment with nibabel installed
To create SEECOG data and a local copy of the program run the following in the terminal:
python /home/nmarkowitz/Documents/IEEG.github.io/preproc/seecog.py <freesurfer_subject_id>
The <freesurfer_subject_id> input is the unique identifier of the freesurfer subject. Alternatively you can give the full path to your freesurfer subject instead of just providing the subject id.
Future Goals
SEECOG is still in active development with many goals. Here are some.
Database-like capabilities
Similar to neurosynth to allow integration of imaging studies and electrode coordinates across studies
Advanced computations
Integrate with websites and softwares for more advanced computations. Check out brainlife
Additional file formats
There are a variety of file formats for neuroimaging and electrophysiology data. - BIDS - NWB - Fieldtrip - Gifti - Freesurfer annotations, labels, curvature - Bioimagesuite mgrid - MNE
Please contact if you would like others to be included on this list
Code Acknowledgements
The following toolboxes contributed to the development of SEECOG:
Contact Us
For questions please reach out to nmarkowitz@northwell.edu or sbickel@northwell.edu