Smoothing Module for Optimization Cranium Segmentation Using 3D Slicer

Anatomy is the most essential course in health and medical education to study parts of human body and also the function of it.  Cadaver is a media used by medical student to study anatomical subject. Because of limited access to cadaver and also due to high prices, this situation makes it necessary to develope an alternative anatomical education media, one of them is the use 3D printing to produce anatomical models. Before 3D Print the cranium, it is necessary to do the segmentation process and often the segmentation result is not good enough and appear a lot of noises. The purpose of this research is  to optimize a 3D cranium based on DICOM (digital imaging and communications in medicine) data processing using the smoothing modules on 3D Slicer. The method of this research is to process the Cranium DICOM data using 3D Slicer software by varying the 5 types of smoothing modules. The results with default parameter fill holes and median have better results compared to others. Kernel size variations are performed for smoothing module fill holes and medians. The result is fill holes get optimal segmentation results using a kernel size of 3 mm and the median is 5 m

Evaluation of natural mandibular shape asymmetry : an approach by using elliptical Fourier analysis

Q2Q1Objectives: The purpose of this study was to demonstrate that asymmetry is a natural occurring phenomenon in the mandibular shape by using elliptical Fourier analysis. Methods: 164 digital orthopantomographs from Colombian patients of both sexes aged 18 to 25 years were collected. Curves from left and right hemimandible were digitized. An elliptical Fourier analysis was performed with 20 harmonics. In the general sexual dimorphism a principal component analysis (PCA) and a hotelling T2 from the multivariate warp space were employed. Exploratory analysis of general asymmetry and sexual dimorphism by side was made with a Procrustes Fit. A non-parametric multivariate analysis of variance (MANOVA) was applied to assess differentiation of skeletal classes of each hemimandible, and a Procrustes analysis of variance (ANOVA) was applied to search any relation between skeletal class and side in both sexes. Results: Significant values were found in general asymmetry, general sexual dimorphism, in dimorphism by side (p < 0.0001), asymmetry by sex, and differences between Class I, II, and III (p < 0.005). However, a relation of skeletal classes and side was not found. Conclusions: The mandibular asymmetry by shape is present in all patients and should not be articulated exclusively to pathological processes, therefore, along with sexual dimorphism and differences between skeletal classes must be taken into account for improving mandibular prediction systems.http://scienti.colciencias.gov.co:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001545804Revista Nacional - Indexad

Three-Dimensional Cone-Beam Computed Tomography Volume Registration for the Analysis of Alveolar Bone Changes

Objectives: 1. Determine accuracy of detecting alveolar bone loss affecting tooth support with registered cone-beam computed tomography (CBCT) compared to intraoral radiographs (IO). 2. Assess repeatability of measurements with CBCT compared to IO. 3. Identify factors which may affect defect detection. 4. Determine effect of bucco-lingual bone thickness on defect detection. Methods: Defects were created in mandibles and imaged pre-, post-defect with IO and CBCT. Six observers viewed IO radiographs pre-, post-defect followed by CBCTs to determine defect presence and extent. Receiver Operating Characteristic (ROC), sensitivity, specificity, logistic regression were used. Inter-, intra-observer agreement were assessed by intraclass correlation coefficient and weighted kappa. Results: Mean ROC Az for CBCT (0.90) was not statistically different from mean Az of IO (0.81). CBCT sensitivity was higher than IO sensitivity (0.85 vs. 0.63, p0.05). Bone thickness, imaging modality, observer had significant effects on bone loss detection. Odds ratio for CBCT vs. IO diagnostic accuracy was 2.29. Odds ratio for bucco-lingual bone thickness was 1.52. There was moderate agreement between observers and substantial agreement within observers for detection of bone loss and measurement of extent. Conclusions: CBCT showed equivalent diagnostic efficacy and specificity for defect detection, but higher sensitivity than IO. CBCT more than doubles the odds of accurate bone loss assessment compared to IO. Odds of bone loss detection increase by approximately 50% per millimeter of bucco-lingual bone loss.Master of Scienc

Similarity index for intuitive assessment of three-dimensional facial asymmetry

Evaluation of facial asymmetry generally involves landmark-based analyses that cannot intuitively assess differences in three-dimensional (3D) stereoscopic structures between deviation and non-deviation sides. This study tested a newly developed similarity index that uses a mirroring technique to intuitively evaluate 3D mandibular asymmetry, and characterised the resulting lower facial soft tissue asymmetry. The similarity index was used to evaluate asymmetry before and after surgery in 46 adult patients (27 men, 19 women; age, 22 ± 4.8 years) with skeletal Class III malocclusion and facial asymmetry who underwent conventional bimaxillary orthognathic surgery. Relative to the midsagittal plane used as the reference plane, the non-overlapping volume of the mandible significantly decreased, and the similarity index significantly increased after surgery. Similarity indexes of the mandible and lower facial soft tissue were strongly negatively correlated with non-overlapping volumes of each measurement. Differences in bilateral hemi-mandibular and hemi-lower facial soft tissue surface and volume measurements before surgery were significantly negatively correlated with similarity indexes of the mandible before and after surgery. This newly developed similarity index and non-overlapping volume using a mirroring technique can easily and intuitively evaluate overall 3D morphological discrepancies, especially 3D mandibular asymmetry, before and after surgery in skeletal Class III patients with facial asymmetry.ope

Assumption-Free Assessment of Corpus Callosum Shape: Benchmarking and Application

Shape analysis provides a unique insight into biological processes. This paper evaluates the properties, performance, and utility of elliptical Fourier (eFourier) analysis to operationalise global shape, focussing on the human corpus callosum. 8000 simulated corpus callosum contours were generated, systematically varying in terms of global shape (midbody arch, splenium size), local complexity (surface smoothness), and nonshape characteristics (e.g., rotation). 2088 real corpus callosum contours were manually traced from the PATH study. Performance of eFourier was benchmarked in terms of its capacity to capture and then reconstruct shape and systematically operationalise that shape via principal components analysis. We also compared the predictive performance of corpus callosum volume, position in Procrustes-aligned Landmark tangent space, and position in eFourier n-dimensional shape space in relation to the Symbol Digit Modalities Test. Jaccard index for original vs. reconstructed from eFourier shapes was excellent (M=0.98). The combination of eFourier and PCA performed particularly well in reconstructing known n-dimensional shape space but was disrupted by the inclusion of local shape manipulations. For the case study, volume, eFourier, and landmark measures were all correlated. Mixed effect model results indicated all methods detected similar features, but eFourier estimates were most predictive, and of the two shape operationalization techniques had the least error and better model fit. Elliptical Fourier analysis, particularly in combination with principal component analysis, is a powerful, assumption-free and intuitive method of quantifying global shape of the corpus callosum and shows great promise for shape analysis in neuroimaging more broadly.Te study was supported by NHMRC of Australia Grant No. 1002160, 1063907 and ARC Grant 130101705. Tis research was partly undertaken on the National Computational Infrastructure (NCI) facility in Canberra, Australia, which is supported by the Australian Commonwealth Government

Surface fluid registration of conformal representation: Application to detect disease burden and genetic influence on hippocampus

abstract: In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistent surface fluid registration, and multivariate tensor-based morphometty (mTBM). First, we conformally map a surface onto a planar rectangle space with holomorphic 1-forms. Second, we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface. Third, we align the feature image with a chosen template image via the fluid image registration algorithm, which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization. The inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images. This alignment induces a corresponding deformation on the surface. We tested the system on Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset to study AD symptoms on hippocampus. In our system, by modeling a hippocampus as a 3D parametric surface, we nonlinearly registered each surface with a selected template surface. Then we used mTBM to analyze the morphometry difference between diagnostic groups. Experimental results show that the new system has better performance than two publicly available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E(is an element of)4 allele (ApoE4), which is considered as the most prevalent risk factor for AD. Our work successfully detected statistically significant difference between ApoE4 carriers and non-carriers in both patients of mild cognitive impairment (MCI) and healthy control subjects. The results show evidence that the ApoE genotype may be associated with accelerated brain atrophy so that our work provides a new MRI analysis tool that may help presymptomatic AD research.NOTICE: this is the author’s version of a work that was accepted for publication in NEUROIMAGE. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Neuroimage, 78, 111-134 [2013] http://dx.doi.org/10.1016/j.neuroimage.2013.04.01

A Comprehensive Survey on Tools for Effective Alzheimer’s Disease Detection

Neuroimaging is considered as a valuable technique to study the structure and function of the human brain. Rapid advancement in medical imaging technologies has contributed significantly towards the development of neuroimaging tools. These tools focus on extracting and enhancing the relevant information from brain images, which facilitates neuroimaging experts to make better and quick decision for diagnosing enormous number of patients without requiring manual interventions. This paper describes the general outline of such tools including image file formats, ability to handle data from multiple modalities, supported platforms, implemented language, advantages and disadvantages. This brief review of tools gives a clear outlook for researchers to utilize existing techniques to handle the image data obtained from different modalities and focus further for improving and developing advanced tools

Morphological Differences of the Articulating Surfaces of Mandibular Condyles in C3H/HeJ and A/J Mice

Characterize the normal variation of the articulating surfaces of mandibular condyle morphologies during periods of growth within and between two strains of mice (A/J and C3H/HeJ) using 3D micro-CT analysis and determine which parts of the microanatomy of the articulating surfaces of the condyle are less susceptible to morphologic variation during skeletal growth. Methods: Cross sectional study utilized micro-CT scans of the condyles of two strains of mice (A/J and C3H/HeJ) at 3-5 wks, 6-8 wks and 9-11 wks of age. Virtual 3D surface models were created, analyzed and computed using shape analysis methods. Results: There is inter-strain variation in condyle morphologies among inbred strains and at each age group. For A/J condylar growth the greatest differences in morphologic change occurs between 3-5 weeks and 6-8 weeks of age with little change thereafter. For the C3H/HeJ strain condylar growth and morphology continued to change beyond 6-8 weeks of age. The anterior and the posterior surfaces of the condyles tended to vary greatest in morphology. Conclusions: Condyles of A/J inbred of mice reach a morphologic plateau around 6-8 weeks of age whereas C3H/HeJ inbred of mice condyles continue morphologic change and growth after 6-8 weeks. Inbred mice despite being isogenic still present shape differences in anatomical structures such as the condyle.Master of Scienc