Craniotomy-induced brain shift#

Authors: Saima Safdar

For craniotomy-induced brain shift, we need a craniotomy region to select the nodes under the craniotomy area on the brain surface. For this we created a module to automatically construct that craniotomy region (see Fig. 1.19{reference-type=”ref” reference=”fig:cran”}). The steps are as follows:

  1. Select the “CranCreator” module.

  2. Select the “Input volume” to create a head mask for pre-operative MRI.

  3. Hit “Apply” to generate the preoperative head mask.

  4. Select the “Input volume” to create a head mask using intra-operative MRI.

  5. Hit “Apply” to generate the intraoperative head mask.

  6. Select the “Select preoperative segment”, which is the head segment generated in step 3.

  7. Select the “Select intraoperative segment”, which is the head segment generated in step 5.

  8. Hit “Apply” to get the craniotomy region.

Patient-specific craniotomy region modeltriangulation.{#fig:cran_2dmodel width=”\textwidth”}

Generate the surface model for this craniotomy region using “Model Maker” module of 3D Slicer. After generating a craniotomy surface model, generate a uniform triangulation of the craniotomy surface model using the “SurfaceTriangulation” module (see Fig. 1.20{reference-type=”ref” reference=”fig:cran_2dmodel”}).

NodeSelector module within 3D Slicer along with patient-specific brainmodel and craniotomy reference geometry for selecting nodes undercraniotomy on brain surface.{#fig:node_sel width=”\textwidth”}

Patient-specific brain model with selected loaded nodes undercraniotomy.{#fig:node_sel2 width=”\textwidth”}

Patient-specific brain model with selected nodes under craniotomy(highlighted red region) in 3D window along with showing nodes (reddots) in axial, sagittal and coronal view. Yellow outline around brainin axial, sagittal and coronal view shows the boundary of the resulting3D patient-specific braingeometry.{#fig:node_sel3 width=”\textwidth”}

NodeSelector module outcome along with 3D brain model and 3Dcraniotomy model in 3D window within 3D Slicer.{#fig:node_sel4 width=”\textwidth”}

Use the “NodeSelector” to select the brain surface nodes under craniotomy region (see Fig. 1.21{reference-type=”ref” reference=”fig:node_sel”}). The steps are as follows:

  1. Select the “NodeSelector” module.

  2. Select the “Input Model to select Nodes”, which is the craniotomy region model.

  3. Select the “Input Brain Model”, which is the patient-specific brain surface triangulated model.

  4. Select the “Output Displaced Nodes”, which is the txt file to save the loaded nodes ids.

  5. Select the “Output Cell Numbers (Triangles)”, which is the txt file containing cell numbers.

  6. Hit “Apply” to get the selected brain nodes (loaded nodes), on which displacements will be applied.

The result for the “NodeSelector” are in Fig. 1.22{reference-type=”ref” reference=”fig:node_sel2”}.

ElectrodesToMarkups module for selecting electrodes within 3D Slicer.{#fig:electrode width=”\textwidth”}