[jxm491]

Thanks for the quick response Andy!

Are all VTA models spherical? Does the imaging characteristics come into play at all with the calculation? Or in general is the same for every subject.

I’m thinking that I will generate the VTA’s in MNI space for all subjects, extract the diameters and create the spheres using FSL. It would be nice to relocalize the electrodes, however I am not as familiar with that process.

[jxm491]

Hi Andy – one more question about the VATs.

I noticed when I open the .nii file the dimensions of the VAT are 25, 30, 30. Unfortunately I need the files to be in the same space as the native images. I noticed that this is the same for the atlas structures that come with the software.

How do I get the VAT in the correct position within the same dimensions as my anatomical image. When I try loading it as a segmentation using ITK snap it doesn’t work (understandably so since the dimensions are not the same). I have been successful overlaying the two images using FSLeyes, but I would really like to have the VAT alone so that I could do comparative analysis with my track density maps using MATLAB.

[jxm491]

Okay – great! Thanks Andy. This was very helpful.

[jxm491]

To clarify – I’m really interested in how I can extract the total volume of activated tissue, not just the percentage of atlas structures affected.

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