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VAT calculation

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / VAT calculation4

Tagged: DTI-space, electrode coordinates, VAT

Viewing 6 posts - 1 through 6 (of 6 total)
  • Author
    Posts
  • 08/10/2017 at 7:49 PM #3105
    jxm491
    Participant

    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

    08/10/2017 at 10:42 PM #3107
    jxm491
    Participant

    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.

    08/15/2017 at 7:49 AM #3145
    andreashorn
    Keymaster

    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

    08/16/2017 at 5:20 PM #3158
    jxm491
    Participant

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

    08/22/2017 at 8:20 PM #3207
    jxm491
    Participant

    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.

    08/22/2017 at 8:32 PM #3209
    andreashorn
    Keymaster

    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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