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BIDS-iEEG Compatibility

Page history last edited by David Groppe 10 months ago

By default, iELVis uses/builds on FreeSurfer's system for organizing files. However, it is also possible for iELVis to read and write files in accordance with the nascent BIDS-iEEG conventions. BIDS-iEEG 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 submitted for publication in mid-December 2018) but here is an example of a study organized according to the current draft of the BIDS-iEEG format:

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

 

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

https://psyarxiv.com/r7vc2/

   

Exporting FreeSurfer Organized iELVis Files into BIDS-iEEG Format:

To copy iELVis electrode information and associate neuroimaging files into BIDS-iEEG 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 BIDS-iEEG Format:

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

 

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

 

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

 

 

Reading Data in BIDS-iEEG Format:

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

plotPialSurf.m

plotAllDepthsOnSlices.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: BIDS-iEEG';
>>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';
>>plotAllDepthsOnSlices('PT001','BIDS-iEEG',cfg);

 

 

 

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