By default, iELVis uses/builds on FreeSurfer's system for organizing files. However, we are now in the process of making it possible for iELVis to also read and write files in accordance with the nascent iEEG-BIDS conventions. iEEG-BIDS is a set of conventions for data storage that facilitates robust and reproducible research as well as data and code sharing. The format may still evolve a bit (the initial standard was just submitted for publication in mid-December 2018) but here is an example of a study organized according to the current draft of the iEEG-BIDS format:

https://github.com/bids-standard/bids-examples/tree/bep010_ieeg/ieeg_motorMiller2007

and here is a preprint of the paper introducing iEEG-BIDS and describing its format:

https://psyarxiv.com/r7vc2/

Exporting FreeSurfer Organized iELVis Files into iEEG-BIDS Format:

To copy iELVis electrode information and associate neuroimaging files into iEEG-BIDS format, simply run iELVisFsurf2BIDS.m, by doing something like this:

>> iELVisFsurf2BIDS('PT001','~/Desktop/HandMotor',1);

Where 'PT001' is the patient's FreeSurfer ID, '~/Desktop/HandMotor', is the BIDS root directory that will be created (if it doesn't already exist) and 1 is the session in which the corresponding iEEG data have been recorded. This will create a sub-PT001 folder than contains electrode locations and information and well as the original raw pre- and post-implant brain volumes used for electrode localization.

The other directories created are subfolders of HandMotor/derivatives/iELVis which contain processed anatomical files (e.g., pial surfaces) used for electrode localization and visualization.

Creating iELVis Files from Scratch in iEEG-BIDS Format:

To create iELVis files in iEEG-BIDS format as well as the FreeSurfer-based format, simply call yangWangElecPjct.m or dykstraElecPjct.m with the optional arguments that specify the iEEG-BIDS root directory and session id. For example:

>>yangWangElecPjct('PT001','~/Desktop/HandMotor',1);

>>dykstraElecPjct('PT001',0,'~/Desktop/FaceMotor',1);

Reading Data in iEEG-BIDS Format:

You can use the following iELVis functions to visualize/process iEEG-BIDS data:

plotPialSurf.m

plotMgridOnSlices.m

For example, this is how you can visualize electrode locations on the cortical surface:

>>cfg=[];
>>cfg.view='l';
>>cfg.figId=1;
>>cfg.elecCoord='LEPTO';
>>cfg.title='PT001: iEEG-BIDS';
>>cfg.bidsDir='~/Desktop/HandMotor';
>>cfgOut=plotPialSurf('PT001',cfg);

And this is how you can visualize depth electrode locations in sets of three 2D slices

>>cfg=[];
>>cfg.printFigs='~/Desktop/SLICE_FIGS';
>>cfg.bidsDir='~/Desktop/HandMotor';
>>plotMgridOnSlices('PT001',cfg);