VAT calculation

[jxm491]

Hello – I am trying to reconstruct the electrodes and VAT using LeadDBS and import them into DTI space.

I have no issues bringing the electrodes into DTI space (since the software gives an output for the electrode coordinates in both MNI and Native space).

However, I am having issue calculate the total volume of activated tissue and bringing that into the native space of the patient since the only statistics I see for the VAT are the cubic mm of volume affected of the atlas structures.

Any help would be greatly appreciate!

Thanks,
Jen

[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.

[andreashorn]

Hi Jen,

sorry for the late response. You can create a VTA in native subject space (just open the 3D visualization tool in native space and create a VTA). The VTAs are saved as nifti files in patientfolder/stimulations/stimulationname/vat_right.nii and /vat_left.nii

These files are in space of your anat_*.nii, postop_tra/cor/sag.nii and rpostop_ct.nii files.

From there, it’s standard neuroimaging stuff, if new to this let me know and I can explain a bit better.

If you’re familiar with any standard neuroimaging pipeline (e.g. SPM or FSL) you could use it to coregister your anat_t1.nii to your b0.nii and port the VTA to DTI space that way. Then extract the values of FA under the mask.

Makes sense?

Best, Andy

[jxm491]

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

[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.

[andreashorn]

Hi,

that’s a simple reslice.
E.g. use

ea_conformspaceto(‘anat_t1.nii’,’vta.nii’);

Of course you loose resolution with this and the above command replaces vta.nii – so make a copy first.

Could also use SPM, FSL or any other neuroimaging software to do this.

Best, Andy

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