Leadfield for Customized Electrodes

[Grace Guo]

Hi ROAST developers and users,

I have a few questions regarding the leadfield feature of ROAST.

(1) By running ROAST with the ‘leadfield’ option on, will the output contain information about the forward matrix, as the matrix A in the paper? 

(2) I noticed that when running ‘leadfield’, the elec72.loc file is automatically used for computation. Is there any chance that customized electrodes can be added to these standard electrodes and the forward matrix be extracted afterwards? What confuses me is that the elec72.loc file seems to contain 2D coordinate information of the electrodes with 10-10 system. Is there any hint for the modification of the loc file and perhaps other parts of the code to contain customized electrodes? (So far I only have the MNI and voxel coordinates for my electrodes).

Thank you so much and I’d really appreciate your help!

Best,
Grace

[Yu (Andy) Huang]

Hi Grace,

1. yes the lead field is saved in the Matlab file ending with *_roastResult.mat

2. yes you can use whatever electrodes you want, but you need to adapt the code. The 2D coordinates in elec72.loc is only for visualization purpose, the actual coordinates (in Cartesian) used are stored in capsInfo.xls spreadsheet. If your electrodes are a subset of those in that spreadsheet, then you can update or create your own .loc file to be used by roast. If they are not part of the spreadsheet, you can still do it by hacking that spreadsheet. Either way you need to adapt the code.

Hope this helps. 

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[Grace Guo]

Hi Andy,

Thank you so much for the advice! I think I manage to place customized electrodes to extract leadfield matrix. This is amazing!

I have some followup-questions regarding the conductivity values.
1) If I’m understanding this correctly, it’s possible to adapt the code to change the conductivity value of each voxel. Specifically, I’m looking into binaryMaskGenerate.m, where each mask matrix is of size (192*253*253) for subject1. I just want to double check that the (x,y,z) voxel coordinate has a certain conductivity (e.g. bone, air) if the value is 1 in the corresponding mask matrix,  and 0 otherwise.
2) Although the simulation result only shows electric field and voltage in the brain,  it seems that the entire MRI scan is included in the computation (i.e. the conductivities in other head regions is also taken into account). Is this understanding correct?

Thank you so much and hope you have a nice day!

Best,
Grace

[Yu (Andy) Huang]

Hi Grace,

Glad to hear you figured it out.

1) Yes, the conductivity is assigned to each segmentation mask.

2) Yes, in total six tissue types are included in the simulation. Visualization only shows the brain by default. 

Hope this helps. 

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