Custom coordinates - which space?

[Grace Edwards]

Hi Andy,

We are stimulating hMT/ Vertex using predetermined coordinates  - i.e. 3 cm dorsal and 5 cm leftward for hMT. Using brainsight, we then localize exactly where the electrodes are in each individual so we can run a simulation using roast(). I have the custom coordinates in MNI space for each participant - what space is roast expecting in the subj_customLocations txt file? 

Thanks,

Grace

[Yu (Andy) Huang]

Hi Grace,

That text file expects coordinates in the voxel space of the original MRI that you'll use to run the simulation. 

Hope this helps.

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[Grace Edwards]

Hi Andy,

I have tried running roast using all the possible coordinates read out from brainsight (brainsight, nifti, MNI - which I converted back to voxel space using MNI2slice.m) on our native space anatomical and the electrodes end up in odd positions - sometimes overlapping or totally off the head (closer to where the neck would be - see the example attached). Do you have any ideas as to what might be happening? I have also attached our coordinates file.

Thanks,

Grace

[Grace Edwards]

Hi Andy,

I'm still trying to figure out my coordinates problem, and it seems that my issue doesn't just lie with the coordinates, so potentially a combination between the coordinates and anatomical? I came to this conclusion by running a simulation using T5 and Cz ("roast([pathnameNative,'/',sub,'.anat.nii'], {'T5',0.75,'Cz',-0.75}, 'electype', {'pad','pad'}, 'elecsize', {[50,50,3],[50,50,3]}, 'simulationTag', 'hMTsimulation_EEG') (see photo1), and navigating in the electric field window (see photo2), I localized a voxel under each of my electrodes to see if I could reproduce the simulation using custom coordinates of provided in voxel space (e.g. T5 at 59,73,128 in photo2). 

Adding these coordinates to my custom locations file, I then ran the a simulation, but I wasn't able to replicate the T5 - Cz simulation instead I got a strange output (photo3)… what do you think could be going on here?

Thanks,

Grace

[Yu (Andy) Huang]

HI Grace,

The problem may be that you did not provide the custom electrode coordinates using the original MRI. ROAST will do some preprocessing if the original MRI is not in standard orientation. So if you want to place electrodes at customized locations, please get the coordinates using the original MRI (the MRI you used to run ROAST). See this example for more information.

Hope this helps. 

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