MS Thesis Defense: Hao Chen

MS Thesis Defense: Reconstruction of Sulcal Geometry in Brain Stimulation Models using Spherical Harmonics

Hao Chen

Location: Zoom Link

Abstract: Over the past few years, there has been increasing interest in transcranial electrical stimulation (tCS) and thus it has been the subject of a growing number of simulation studies. Indeed, some federal agencies in the US now require model-based simulations to be included as part of tCS grant proposal. In order to obtain more accurate simulation results and guide the relevant research, it is of important to assess the impact of the accuracy of the anatomical 3D brain model that these studies depend on. However, due to the partial volume problem, many 3D reconstruction results based on MR images are inaccurate with respect to the details of the geometry of the sulci. Specifically, when the sulci are on the scale of, or even smaller than, the voxel resolution of the MRI, these models generally really in a binary approximation, either making the sulcus wider in the model than in reality or eliminating it altogether. In this thesis, we describe a method for modeling the 3D reconstruction of the brain that may facilitate controlled study of the effect of these approximations. The general approach is to model the brain surface using a spherical harmonic expansion, then modify the expansion coefficients in an attempt to selectively and smoothly control sulcal width. In the first part of the thesis, we describe and evaluate an approach in which we experimentally selected two groups of spherical harmonic coefficients within a specified range that could simultaneously affect a chosen sample of the gyri. For the coefficients in the first group, the widths of all gyri in the sample were increased by enlarging the corresponding coefficients for each spherical harmonic. Conversely, for each coefficient in the second group, this adjustment caused the widths of the sampled gyri to decrease simultaneously. We evaluated the method by alternately increasing / decreasing the coefficients in the first group, and decreasing / increasing those in the second, by a chosen range of factors, and observing the effects on the model cortical surface. Experimental results showed that the widths of most of the sulci and gyri were simultaneously adjusted according to the desired effect.
In the second part of the thesis, we tried to build a volume mesh starting from the modified spherical harmonic surfaces. It turned out that this problem was particularly challenging because most of the surface models in our study had self-intersection points. We used a well-known software package for mesh processing, iso2mesh, to successfully remove the self-intersection points on all surfaces were removed finally, but this process seemed to create small holes in the surfaces of the models. Despite these holes, with a few exceptions, the widths of most sulci (gyri) were still simultaneously increased (decreased) with the coefficient adjustments. This result provides a direction for further study towards controlled study of the influence of the partial volume problem on modeling of tCS.