seek_localize (Stereotactic ElectroEncephalography Kit)¶

seek_localize helps localize iEEG electrodes on MRI/CT images and deals with data processing for iEEG-BIDS data.

Documentation¶

The documentation can be found under the following links:

for the stable release
for the latest (development) version

To see the seek documentation, see http://neuroseek.azurewebsites.net/docs/seek/

Setup and Installation¶

See INSTALLATION GUIDE for full instructions. A quick setup can occur with github and pipenv. This has been tested on Python versions 3.7, 3.8 and 3.9.

# clone repository locally
$ git clone https://github.com/adam2392/seek_localize
$ python3.8 -m venv .venv
$ pipenv install

Through pip

$ pip install seek_localize

Quick Usage¶

Here is a quick look at a basic use-case, where we want to label the anatomical regions each electrode is in, based on FreeSurfer.

from seek_localize import label_elecs_anat
from mne_bids import BIDSPath

# define file path to the T1w image that electrode coordinates are localized in
img_fname = ...

# define a path to the electrodes.tsv file in iEEG-BIDS
bids_path = BIDSPath(..., suffix='electrodes', extension='.tsv')

# define filepath to the FreeSurferColor Look up Table
# (it is stored locally)
fs_lut_fpath = seek_localize.fs_lut_fpath

label_elecs_anat(bids_path, img_fname, fs_lut_fpath)

Data Organization¶

We use BIDS. See https://github.com/bids-standard/bids-starter-kit/wiki/The-BIDS-folder-hierarchy for more information. We recommend the following BIDS structure with the minimally required set of files.

{bids_root}/
     /sub-001/
         /anat/
             - sub-001_*_T1w.nii
         /ct/
             - sub-001_*_CT.nii
         /ieeg/
             - sub-001_*_channels.tsv
             - sub-001_*_electrodes.tsv
             - *

Development¶

seek_localize was created and is maintained by Adam Li. It is also maintained and contributed by Christopher Coogan and other researchers in the NCSL and Crone lab. Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request! See the contribution guide.

To report a bug, please visit the GitHub repository.

Note that this program is provided with NO WARRANTY OF ANY KIND. If you can, always double check the results with a human researcher, or clinician.

How to cite?¶

If you want to cite seek_localize, please cite the following paper(s).

Adam Li. (2021, February 5). seek_localize (Version 0.0.1). Zenodo. http://doi.org/10.5281/zenodo.4508674

Acknowledgement¶

Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A., & Jas, M. (2019): MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software, 4:1896. DOI: [10.21105/joss.01896](https://doi.org/10.21105/joss.01896)

FAQ¶

1. For ECoG data, we do not explicitly have a process outlined, but these are significantly easier since grids can be easily interpolated. See Fieldtrip Toolbox.