08/10/2017 at 7:49 PM #3105
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!
Jen08/10/2017 at 10:42 PM #3107
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 #3145andreashornKeymaster
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.
Best, Andy08/16/2017 at 5:20 PM #3158
Okay – great! Thanks Andy. This was very helpful.08/22/2017 at 8:20 PM #3207
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 #3209andreashornKeymaster
that’s a simple reslice.
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.
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