Apr 10, 2024

Public workspaceAssessment of implant accuracy using high-resolution postmortem MRI

DOI
dx.doi.org/10.17504/protocols.io.14egn6x86l5d/v1
  • 1University of Pittsburgh
Lucy Liang
Open access
DOI: dx.doi.org/10.17504/protocols.io.14egn6x86l5d/v1
Protocol Citation: Lucy Liang, Elvira Pirondini, Jonathan C Ho 2024. Assessment of implant accuracy using high-resolution postmortem MRI. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn6x86l5d/v1
Manuscript citation:
Liang, L., Zimmermann Rollin, I., Alikaya, A., Ho, J.C., Santini, T., Bostan, A.C., Schwerdt, H.N., Stauffer, W.R., Ibrahim, T.S., Pirondini, E., Schaeffer, D.J., 2024. An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys. BioRxiv https://doi.org/10.1101/2024.02.17.580767
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 26, 2024
Last Modified: May 31, 2024
Protocol Integer ID: 97399
Keywords: ASAPCRN, postmortem, implant accuracy, non-human primate, MRI
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020519
Abstract
Deep brain implant accuracy is important for successful experiments in non-human primates. In this protocol, we describe the steps to use postmortem imaging to assess the accuracy of an implant by visualizing implant location with a small thermal ablation and comparing its coordinates to image based pre-surgical planning.

This protocol is supplementary to the manuscript:
Liang, L., Zimmermann Rollin, I., Alikaya, A., Ho, J.C., Santini, T., Bostan, A.C., Schwerdt, H.N., Stauffer, W.R., Ibrahim, T.S., Pirondini, E., Schaeffer, D.J., 2024. An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys. BioRxiv https://doi.org/10.1101/2024.02.17.580767
Materials
Thermal Ablation
  • Radiofrequency cannula (S-100 5 mm ActiveTip Straight cannula 22G, Abbott)
  • Radiofrequency electrode (RF-SE-10 Reusable Stainless Steel Electrode, Abbott)
  • Grounding pad (Abbott)
  • Radiofrequency generator (NeuroTherm NT 1100, Abbott)

Imaging Equipment
  • 9.4T/31 cm horizontal-bore Bruker AV3 HD animal scanner

Tissue Preparation
  • Euthanasia drug (Fetal Plus or equivalent)
  • Perfusion machine
  • 1x phosphate buffered saline (PBS)
  • 4% paraformaldehyde (PFA)
  • Brain dissection tools

Image Processing Software
  • FSL (Smith et al. 2004)

S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R.K. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews, Advances in functional and structural MR image analysis and implementation as FSL Neuroimage, 23 (2004), pp. S208-S219
https://doi-org.pitt.idm.oclc.org/10.1016/j.neuroimage.2004.07.051
Before start
Follow this protocol after all terminal experiments have been completed, but before euthanizing the animal.

Note: Perfusion with 4% PFA may cause some degree of tissue shrinkage. We observed an average of 3.3% shrinkage with our brain tissue.
Thermal ablation & tissue preparation
Thermal ablation & tissue preparation
Before euthanizing the animal according to protocol, perform a thermal lesion through the deep brain electrode.

We use a radiofrequency cannula (S-100 5 mm ActiveTip Straight cannula 22G, Abbott) and a radiofrequency electrode (RF-SE-10 Reusable Stainless Steel Electrode, Abbott), with a radiofrequency generator (NeuroTherm NT 1100).

Parameters: ~80℃, 1min
Remove electrode (not MR compatible) from the brain and euthanize the animal.
Perfuse transcardially with 1x phosphate buffered saline (PBS), followed by 4% paraformaldehyde (PFA).
Dissect out the brain with care. Carefully remove the dura and any blood clots from the surface of the brain.
Place the brain in 4% PFA for an additional 24 hours, then, move to 1x PBS.
Imaging and implant error calculation
Imaging and implant error calculation
Collect T2 or T2* weighted images of the brain in a 9.4 T/31 cm horizontal-bore Bruker AV3 HD animal scanner with the following parameters:
T2: 125 μm isotropic,TR/TE = 1500/60ms, FOV = 52×80×56 mm
T2*: 80 μm isotropic, TR/TE = 100/16 ms, FOV = 55×70×45 mm
Visualize the images in FSL, and align the anterior commissure to posterior commissure (ACPC) line with the x-axis of the mid sagittal plane with the FLIRT function.
Identif y the tip of the electrode (at the center of the thermal lesion) within the internal capsule (or your target of interest), and record the coordinates.

Calculate the Xi, Yi, and Zi distance (in pixels) from the posterior commissure (PC) point. Convert to metric distance using pixel resolution.

(coordinate subscript "i" indicates implant coordinates, "t" indicates target coordinates)
Calculate target implant error in each axis by subtracting implant coordinates and target coordinates (e.g. Xe = Xi - Xt)
Finally, calculate the overall target implant error (IE) using Euclidean distance IE = sqrt(Xe2+Ye2+Ze2)

Protocol references
Liang, L., Zimmermann Rollin, I., Alikaya, A., Ho, J.C., Santini, T., Bostan, A.C., Schwerdt, H.N., Stauffer, W.R., Ibrahim, T.S., Pirondini, E., Schaeffer, D.J., 2024. An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys. BioRxiv https://doi.org/10.1101/2024.02.17.580767

S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R.K. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews, Advances in functional and structural MR image analysis and implementation as FSL Neuroimage, 23 (2004), pp. S208-S219 https://doi-org.pitt.idm.oclc.org/10.1016/j.neuroimage.2004.07.051