seek-localize 0.2.0

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
             - *