A MRI-Based Toolbox for Neurosurgical Planning in Nonhuman Primates

This protocol is significant to the neural engineering field because it offers a concise and unimodal procedure designed to enhance the precision and safety of neurosurgery in non-human primates. This technique offers researchers the unique ability to visualize every aspect of their implantation or injection procedure, and ensures that they can enter an operating room as prepared as possible. Visual demonstration of this method is critical because it highlights the impact and clarity that life-size physical models can have on surgical planning.

To extract the brain in the magnetic resonance imaging software, open the plugins drop-down menu and select extract brain. Set the extraction intensity threshold at 2.5, 2.7 and the threshold gradient value to zero. After creating a bitmap of the brain image, select build surface under the image menu and input the threshold used to create the bitmap containing the region of interest.

Then click okay to create the surface. And save the extracted brain region of interest as a NII or NII. GZ file.

To generate a brain model, open the extracted brain file in the appropriate medical image processing software. And in the editor module menu, select threshold effect, adjust the threshold range sliders so the portion of the bitmap containing the brain is highlighted in all three slices. Open the model maker module and in the input volumes dropdown menu, select the bitmap file.

Under models, select create new model hierarchy and click apply to create the volume. When the imported mesh brain surface has been imported, select graphic one. And suppress any unnecessary graphic features until only the features containing the brain are remaining in the file.

Then, save the files in the PRT format for further manipulation, and as an STL for 3D printing. For brain molding, load the extracted brain model into an appropriate computerated design software program. Under the features section of the insert menu select convert to mesh body and the graphic body of the brain to convert it, and open this sketch tab and click sketch to select the top plane as the sketch plane.

Draw a rectangle around the entire hemisphere of interest, and select the extrude boss base feature to extrude a cubic rectangle containing the top part of the brain. Under the features section of the insert menu, select convert to mesh body and select the extruded cube in the solid bodies folder to convert it. To create the negative space, use the combine feature and select the subtract option to subtract the model of the brain from the newly extruded cube.

For skull modeling, import the quick MPRAGE MRI into an appropriate matrix manipulation software program as a DICOM file. And use the commands to combine all of the frames into a single 3D matrix as necessary. Ensure that each 2D frame of the matrix displays a coronal slice and use a greater than operator for individual pixel values to threshold the 3D matrix to create a binary mask.

Then adjust the threshold such that the skull anatomy is captured by the mask. To remove the musculature layer, iteratively grab a 2D slice from the mask to process each frame from the 3D mask separately, and use the tilde operator to invert the values of the mask. The skull values will be ones.

The outside and brain will have values of zero. Add additional empty voxels to the 3D mask until the lowest resolution dimension of the mask is larger by a factor defined by the scale factor. And linearly interpolate values in the mask until the mask fills the new space.

Then, export the skull as an STL file, or a similar file type for 3D printing. To create a craniotomy in the 3D skull model, open the MRI file and manually scan back and forth through the 3D matrix to identify the approximate location of the craniotomy using anatomical landmarks found in the macaque brain atlas. To create an agarose mold, pour agarose solution into a full or half hemisphere brain mold and allow the solution to solidify within the mold for about two hours.

When the agarose has set, use a spatula to gently remove the gel model from the mold, taking care, not to damage the surface of the mold. For a mock infusion of the agarose gel model, mount a syringe pump onto a stereotaxic arm on a stereotaxic frame and fill a 250 microliter syringe with the ionized water. Load the syringe onto the syringe pump and completely fill the injection cannula with the water.

Use the pump driver to load the target volume of food coloring into the syringe for injection. And eject the food coloring until a small bead forms at the tip of the cannula. Dry the bead from the cannula tip and position the gel model under the cannula.

Lower the cannula until the tip touches the surface of the gel model, and note the measurements on the stereotaxic arm. Then smoothly and quickly lower the cannula into the gel model to the target injection depth. Making sure that the surface of the gel has sealed around the cannula and run the pump while observing the spread of the die until the target volume has been delivered.

Using this protocol, an anatomically accurate physical model of the non-human primate brain can be created. Similarly, an anatomically accurate physical model of the primate skull extracted from magnetic resonance images can also be generated. The physical models of the skull and brain can be combined with a tight interference fit, validating the accuracy of the two models relative to each other and legitimizing the extrapolated MRI analysis data.

The insertion of a craniotomy into the skull prior to printing, allows combination of all of the parts of the sample interface for evaluation of the geometry of various components in relation to the skull and brain. For example, in this experiment, the feet of the head post were manipulated and fitted to the curvature of the skull at the location of the implantation prior to the procedure. Resulting in a reduced surgical time from approximately 2.5 hours to one hour from opening to implantation, greatly reducing the risk of operative complications.

Agarose mixture brain models can be injected with yellow dye in an area of interest to estimate the volume of the proposed infusion and combining the agarose model with a 3D printed skull can be used to model viral vector injection surgery. Taking into account the variations in skull and brain anatomy in different animals, success in the extraction process will require adjustments in the iterative steps. So this toolbox can be used to reduce risk in non-human primate neurosurgery and the fabrication techniques can enhance the experimental process at the cutting edge of neuroscience.