Biomedical subjects

Jimin Liu

Publications and source records attributed to Jimin Liu.

4 recordsLinked to original sources

PubMed2006

Correlation between the anatomical and functional human subthalamic nucleus.

This work addresses the spatial correlation between the anatomical and functional human subthalamic nucleus (STN). The anatomical STN (A-STN), derived from the Schaltenbrand-Wahren brain atlas, is histology based. The functional STN (F-STN) is probabilistic, constructed from neuroelectrophysiological and neuroimaging data of 184 Parkinson's disease patients. The A-STN and F-STN are placed in the same space and compared in terms of mutual relative overlapping of anatomy with function. The F-STN and A-STN correlate well for medium and high probabilities of the F-STN. For probability p >or= 0.3, >95% of F-STN is inside the A-STN, and for p >or= 0.5, the complete F-STN is inside the A-STN for each left and right STN. Therefore, the F-STN for p = 0.5 can potentially be used for identification of the STN in neuroimages.

Anatomy, Artistic↗

PubMed2006

Quantification and visualization of three-dimensional inconsistency of the globus pallidus internus in the Schaltenbrand-Wahren brain atlas.

The major shortcomings of the Schaltenbrand-Wahren (SW) brain atlas include 3-dimensional (3D) inconsistency and spatial sparseness. This work quantifies and visualizes 3D inconsistency of the globus pallidus internus (GPi), a stereotactic target for the treatment of Parkinson's disease, dystonia and Huntington disease. The GPi 3D models 3D-A, 3D-C and 3D-S are reconstructed from the SW axial, coronal and sagittal microseries, respectively, by applying a shape-based (Nonuniform Rational B Splines) method. All three 3D models, placed in the SW coordinate system, are compared quantitatively in terms of location (centroids), size (volumes), shape (normalized eigen values), orientation (eigen vectors) and mutual spatial relationships (overlaps and inclusions). The analysis is done in 3D within each orientation and across them. The reconstructed 3D GPi models substantially differ in location, size and inclusion rate. The centroid of 3D-C is located more medially (15.6 mm) than those of 3D-A (17.5 mm) and 3D-S (18.2 mm), and that of 3D-A more ventrally (-2.3 mm) than those of 3D-C (-0.1 mm) and 3D-S (-0.4 mm). 3D-S has the smallest volume (347.3 mm3); 3D-A is 1.18 and 3D-C 1.85 times larger. The highest inclusion rate is for 3D-S (54.3 and 56.3%) and the lowest for 3D-C (28.8 and 30.6%). A smaller variability is observed in shape, orientation and overlap size (196.8, 196.1 and 185.5 mm3). To get a better correspondence between 3D-C and 3D-S, the coronal microseries were scaled laterally by 1.1667. This results in a substantial improvement of the inclusion rate of 3D-S (87.9%), though raising the volume mismatch to 2.16. The GPi in the SW atlas has a substantial 3D inaccuracy within each orientation and across them. Therefore, absolute and direct reliance on the original atlas is unsafe, and this atlas has to be used with great care and understanding of its limitations. As matching various SW microseries by global scaling is not feasible, we propose the target-dependent scaling based on structure centroid matching.

Brain↗

PubMed2006

Quantification and visualization of the three-dimensional inconsistency of the subthalamic nucleus in the Schaltenbrand-Wahren brain atlas.

The Schaltenbrand-Wahren (SW) brain atlas has many limitations: the major two are three-dimensional (3D) inconsistency and spatial sparseness. In this work, we quantify and visualize the 3D inconsistency of the subthalamic nucleus (STN). The STN 3D models, 3D-A, 3D-C and 3D-S, are reconstructed from the SW axial, coronal, and sagittal microseries, respectively, by using a shape-based (NURBS) approach. All three models are placed in the SW coordinate system and compared quantitatively in terms of location (centroids), size (volumes), shape (normalized eigenvalues), orientation (eigenvectors), and mutual spatial relationships (overlaps and inclusions). Analysis is done in 3D within each orientation and across them. A dedicated tool is developed for quantitative validation of 3D modeling. The average error achieved is 0.088 mm, which is at the resolution limit of the digital SW atlas. The reconstructed 3D STN models differ in location, size, shape, orientation, overlap size, and inclusion rate. The 3D-S volume is 1.27 times larger than that of 3D-A and 1.38 times larger than that of 3D-C. The highest overlap size is found between 3D-A and 3D-S. The highest inclusion rates of 52.5 and 66.6% are for 3D-A and 3D-S. 3D-C has the lowest overlap size and results in the lowest inclusion rates (around 20-30%), meaning that 3D-C is substantially displaced in comparison to 3D-A and 3D-S. The lateral centroid coordinate of 3D-C is 9.18 mm while that of 3D-S is 12.17 mm. Each of the 3D models has some limitation: 3D-A in orientation, 3D-C in location, and 3D-S in shape realism. The STN in comparison to the actual almond is smaller, and relatively (i.e. normalized to the same height) 2.2-2.4 times wider and 3.7-5.5 times longer. 3D-C becomes more similar to 3D-S by scaling the SW coronal microseries laterally by 1.3257. Then the lateral coordinates of their centroids coincide, the difference between them in orientation is 0.11 mm, and 3D-S is only 1.06 times larger than the scaled 3D-C. This operation substantially improves registration of the SW atlas with the probabilistic functional atlas. However, 3D visualization shows that both 3D-S and scaled 3D-C models are heavily interwoven resulting in low inclusion rates of about 60%. The STN in the SW atlas shows severe 3D inaccuracy within each orientation and across them, and it has to be employed with great care and understanding of its limitations.

Anatomy, Artistic↗

PubMed2006

A hybrid approach to shape-based interpolation of stereotactic atlases of the human brain.

Stereotactic human brain atlases, either in print or electronic form, are useful not only in functional neurosurgery, but also in neuroradiology, human brain mapping, and neuroscience education. The existing atlases represent structures on 2D plates taken at variable, often large intervals, which limit their applications. To overcome this problem, we propose a hybrid interpolation approach to build high-resolution brain atlases from the existing ones. In this approach, all section regions of each object are grouped into two types of components: simple and complex. A NURBS-based method is designed for interpolation of the simple components, and a distance map-based method for the complex components. Once all individual objects in the atlas are interpolated, the results are combined hierarchically in a bottom-up manner to produce the interpolation of the entire atlas. In the procedure, different knowledge-based and heuristic strategies are used to preserve various topological relationships. The proposed approach has been validated quantitatively and used for interpolation of two stereotactic brain atlases: the Talairach-Tournoux atlas and Schaltenbrand-Wahren atlas. The interpolations produced are of high resolution and feature high accuracy, 3D consistency, smooth surface, and preserved topology. They potentially open new applications for electronic stereotactic brain atlases, such as atlas reformatting, accurate 3D display, and 3D nonlinear warping against normal and pathological scans. The proposed approach is also potentially useful in other applications, which require interpolation and 3D modeling from sparse and/or variable intersection interval data. An example of 3D modeling of an infarct from MR diffusion images is presented.

Algorithms↗