01/11/2019 at 12:58 AM #6315weaverkParticipant
I want to echo the general sentiments on this forum. lead DBS is a remarkable program, one that has made my life a lot easier. So thank you.
I have 2 questions. I am wanting to work with the VAT models.
1) Is there a way to render a group image that loads VAT models from multiple subjects onto a single background (e.g. MNI ICBM) image?
2) I am also wanting to parcellate the tissue types within each VAT model, however in native space. I have found the nifti VAT files within the simulations sub-directly. However, to get this back into native space, I have had trouble figuring out the base image that the VAT nifti is rendered on. That is, to apply a reverse registration matrix, I need an anatomical image (preferably T1) with the same resolution as the VAT image (e.g., .17 x .17 x. .21).
Kurt01/11/2019 at 2:14 AM #6316weaverkParticipant
Actually, apologies, for question 2, I just realized I can render the VAT into native space to begin with then re-slice the image to native resolution.
But for question 1, I really would like to generate a group map with the electrodes and VAT models in normalized space.
Thanks again01/11/2019 at 9:18 AM #6317andreashornKeymaster
thanks for your kind words. And yes, I’d solve question 2 exactly as you would – since the resolution of the VTAs is so good a reslice to the anchor preop image (often the T1) won’t harm them and we never felt the need to export one in that resolution.
Re q 1, two options:
1. In Lead Group create a new variable with one entry for each patient (the default) and fill it with ones (e.g. put a 1 into each row). Then check “Map regressor to VATs”, select all patients and click visualize 3D. This will create a nifti file (in the lead group directory) that is the group’s VTA. It will also visualize the group VTA in the 3D viewer directly.
2. Second option is to just create it with e.g. SPM imcalc or fslmaths. In SPM imcalc, select a template (e.g. MNI space) first and then all VTAs. Then only use i2, i3, i4.. (ignore i1, i.e. the template) in your expression. The result will still be exported in MNI space (i.e. in the same resolution of i1, the template you selected).
If you have the joint VTA as a nifti file (which will result from either solution 1 or 2) then you can always display that (or any other nifti file) in the lead DBS 3D viewer by choosing Add Objects -> Add Roi.
Hope this helps!
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