Name: three-dimensional shape modeling and analysis of brain structures
Uploaded: 2019-11-14T10:00:00
Description: Watch this Scientific Journal Video about Three-Dimensional Shape Modeling and Analysis of Brain Structures at JoVE.com

The work was funded by the National Research Foundation of Korea (JP as the PI). JK is funded by Kyungpook National University Research Fund; and MCVH is funded by the Row Fogo Charitable Trust and the Royal Society of Edinburgh. The hippocampal segmentation was adapted from in-house guidelines written by Dr. Karen Ferguson, at the Centre for Clinical Brain Sciences, Edinburgh, UK.

Brain MR images were acquired as per the protocol approved by the local institutional review board and ethics committee.
NOTE: The tools for shape modeling and analysis can be downloaded from the NITRC repository: <a href="https://www.nitrc.org/projects/dtmframework/" target="_blank">https://www.nitrc.org/projects/dtmframework/</a>. The GUI software (DTMModeling.exe) can be executed after extraction.<!--The publication list on the shape modeling tools can be found in the proje...

<ol>
	<li>Costafreda, S. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+hippocampal+shape+analysis+predicts+the+onset+of+dementia+in+mild+cognitive+impairment.">Automated hippocampal shape analysis predicts the onset of dementia in mild cognitive impairment.</a> NeuroImage. 56 (1), 212-219 (2011).</li><li>Platero, C., Lin, L., Tobar, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Longitudinal+Neuroimaging+Hippocampal+Markers+for+Diagnosing+Alzheimer's+Disease.">Longitudinal Neuroimaging Hippocampal Markers for Diagnosing Alzheimer's Disease.</a> Neuroinformatics. , 1-19 (2018).</li><li>Vald&#233;s Hern&#225;ndez, M. D. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rationale,+design,+and+methodology+of+the+image+analysis+protocol+for+studies+of+patients+with+cerebral+small+vessel+disease+and+mild+stroke.">Rationale, design, and methodology of the image analysis protocol for studies of patients with cerebral small vessel disease and mild stroke.</a> Brain and behavior. 5 (12), e00415 (2015).</li><li>Kalmady, S. V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+correlates+of+hippocampus+volume+and+shape+in+antipsychotic-na&#239;ve+schizophrenia.">Clinical correlates of hippocampus volume and shape in antipsychotic-na&#239;ve schizophrenia.</a> Psychiatry Research: Neuroimaging. 263, 93-102 (2017).</li><li>Kim, J., Vald&#233;s Hern&#225;ndez, M. D. C., Royle, N. A., Park, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hippocampal+Shape+Modeling+Based+on+a+Progressive+Template+Surface+Deformation+and+its+Verification.">Hippocampal Shape Modeling Based on a Progressive Template Surface Deformation and its Verification.</a> IEEE Transactions on Medical Imaging. 34 (6), 1242-1261 (2015).</li><li>Kim, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+shape+analysis+of+the+brain's+third+ventricle+using+a+midplane+encoded+symmetric+template+model.">3D shape analysis of the brain's third ventricle using a midplane encoded symmetric template model.</a> Computer Methods and Programs in Biomedicine. 129, 51-62 (2016).</li><li>Kim, J., Ryoo, H., Vald&#233;s Hern&#225;ndez, M. D. C., Royle, N. A., Park, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brain+Ventricular+Morphology+Analysis+Using+a+Set+of+Ventricular-Specific+Feature+Descriptors.">Brain Ventricular Morphology Analysis Using a Set of Ventricular-Specific Feature Descriptors.</a> International Symposium on Biomedical Simulation. , 141-149 (2014).</li><li>Vald&#233;s Hern&#225;ndez, M. D. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hippocampal+morphology+and+cognitive+functions+in+community-dwelling+older+people:+the+Lothian+Birth+Cohort+1936.">Hippocampal morphology and cognitive functions in community-dwelling older people: the Lothian Birth Cohort 1936.</a> Neurobiology of Aging. 52, 1-11 (2017).</li><li>Lee, P., Ryoo, H., Park, J., Jeong, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+and+Microstructural+Changes+of+the+Hippocampus+in+Early+MCI:+A+Study+Utilizing+the+Alzheimer's+Disease+Neuroimaging+Initiative+Database.">Morphological and Microstructural Changes of the Hippocampus in Early MCI: A Study Utilizing the Alzheimer's Disease Neuroimaging Initiative Database.</a> Journal of Clinical Neurology. 13 (2), 144-154 (2017).</li><li>Cox, S. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Associations+between+hippocampal+morphology,+diffusion+characteristics,+and+salivary+cortisol+in+older+men.">Associations between hippocampal morphology, diffusion characteristics, and salivary cortisol in older men.</a> Psychoneuroendocrinology. 78, 151-158 (2017).</li><li>Sled, J. G., Zijdenbos, A. P., Evans, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+nonparametric+method+for+automatic+correction+of+intensity+nonuniformity+in+MRI+data.">A nonparametric method for automatic correction of intensity nonuniformity in MRI data.</a> IEEE Transactions on Medical Imaging. 17 (1), 87-97 (1998).</li><li>Tustison, N. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=N4ITK:+improved+N3+bias+correction.">N4ITK: improved N3 bias correction.</a> IEEE Transactions on Medical Imaging. 29 (6), 1310-1320 (2010).</li><li>Zhang, Y., Brady, M., Smith, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Segmentation+of+brain+MR+images+through+a+hidden+Markov+random+field+model+and+the+expectation-maximization+algorithm.">Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm.</a> IEEE Transactions on Medical Imaging. 20 (1), 45-57 (2001).</li><li>Wardlaw, J. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brain+aging,+cognition+in+youth+and+old+age+and+vascular+disease+in+the+Lothian+Birth+Cohort+1936:+rationale,+design+and+methodology+of+the+imaging+protocol.">Brain aging, cognition in youth and old age and vascular disease in the Lothian Birth Cohort 1936: rationale, design and methodology of the imaging protocol.</a> International Journal of Stroke. 6 (6), 547-559 (2011).</li><li>Morey, R. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+automated+segmentation+and+manual+tracing+for+quantifying+hippocampal+and+amygdala+volumes.">A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes.</a> NeuroImage. 45 (3), 855-866 (2009).</li><li>Boccardi, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Survey+of+protocols+for+the+manual+segmentation+of+the+hippocampus:+preparatory+steps+towards+a+joint+EADC-ADNI+harmonized+protocol.">Survey of protocols for the manual segmentation of the hippocampus: preparatory steps towards a joint EADC-ADNI harmonized protocol.</a> Journal of Alzheimer's Disease. 26 (s3), 61-75 (2011).</li><li>Winterburn, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+In+Vivo+Manual+Segmentation+Protocol+for+Human+Hippocampal+Subfields+Using+3T+Magnetic+Resonance+Imaging.">High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging.</a> Journal of Visualized Experiments. (105), e51861 (2015).</li><li>MacLullich, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intracranial+capacity+and+brain+volumes+are+associated+with+cognition+in+healthy+elderly+men.">Intracranial capacity and brain volumes are associated with cognition in healthy elderly men.</a> Neurology. 59 (2), 169-174 (2002).</li><li>Gower, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generalized+Procrustes+analysis.">Generalized Procrustes analysis.</a> Psychometrika. 40 (1), 33-51 (1975).</li><li>Lorensen, W. E., Cline, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Marching+cubes:+A+high+resolution+3D+surface+construction+algorithm.">Marching cubes: A high resolution 3D surface construction algorithm.</a> ACM Siggraph Computer Graphics. , 163-169 (1987).</li></ol>

In summary, we have described the software pipeline for the shape analysis on brain structures including (1) MR image segmentation using open tools (2) individual shape reconstruction using a deformable template model, and (3) quantitative shape difference measurement via transitive shape correspondence with the template model. Statistical analysis under the false discovery rate (FDR) correction is performed with the shape deformity to investigate the significance of morphological changes of brain structures, associated ...

Shape analysis of brain structures has emerged as the preferred tool to investigate their morphological changes under pathological processes, such as neurodegenerative diseases and aging1. Various computational methods are required to 1) accurately delineate the boundaries of target structures from medical images, 2) reconstruct the target shape in the form of 3D surface mesh, 3) build inter-subjects correspondence across the individual shape models via shape parameterization or surface registration, and 4) quantitatively assess the regional shape differences between individuals or groups. Over the past several years, many methods have been introduced in neuroimaging studies for each of these steps. However, despite the remarkable developments in the field, there are not many frameworks immediately applicable to research. In this article, we describe each step of the shape analysis of brain structures using our custom shape modeling tools and publicly available image segmentation tools.
Here, we demonstrate the shape analysis framework for brain structures through the shape analysis of the left and right hippocampi using a dataset of adult controls and Alzheimer&#39;s disease patients. Atrophy of the hippocampi is recognized as a critical imaging biomarker in neurodegenerative diseases2,3,4. In our shape analysis framework, we employ the template model of the target structure and the template-to-image deformable registration in the shape modeling process. The template model encodes general shape characteristics of the target structure in a population, and it also provides a baseline for quantifying the shape differences among the individual models via their transitive relation with the template model. In the template-to-image registration, we have developed a Laplacian surface deformation method to fit the template model to the target structure in individual images while minimizing the distortion of the point distribution in the template model5,6,7. The feasibility and robustness of the proposed framework have been validated in recent neuroimaging studies of cognitive aging8, early detection of mild cognitive impairment9, and to explore associations between brain structural changes and cortisol levels10. This approach would make it easier to use the shape modeling and analysis methods in further neuroimaging studies.

three-dimensional shape modeling and analysis of brain structures

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. We have developed a software package for accurate and robust shape modeling and group-wise analysis. Here, we introduce an pipeline for the shape analysis, from individual 3D shape modeling to quantitative group shape analysis. We also describe the pre-processing and segmentation steps using open software packages. This practical guide would help researchers save time and effort in 3D shape analysis on brain structures.

The shape modeling process described here has been employed for various neuroimaging studies on aging6,8,10 and Alzheimer&#39;s disease5,9. Especially, this shape modeling method showed its accuracy and sensitivity in the shape analysis on the hippocampus for an aging population of 654 subjects8. A quantitative ana...

Watch this Scientific Journal Video about Three-Dimensional Shape Modeling and Analysis of Brain Structures at JoVE.com

Three-Dimensional Shape Modeling and Analysis of Brain Structures

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. ...

Accurately recovering the shape features against rough and noisy segmentations is critical to achieving good anatomical correspondence between individual brain shape models. Our framework provides various tools for individual shape modeling, group-wise template construction, and shape deformity computation. And it has been used for large datasets of the human brain.Demonstrating this procedure will be Dr.Jaeil Kim, a former grad student from my laboratory who developed the software for the brain shape modeling. For manual editing of the hippocampal segmentation, open the T1 weight magnetic resonance image and the automatic hippocampal segmentation results in the graphic user interface software. Click the icon in the display window to select the coronal view and scroll through the volume until the uncus is located.Including the uncus in the hippocampal mask where it is present, use the add and subtract functions to edit the mask of the hippocampal body after the uncus has receded. Continue editing the hippocampal mask until the hippocampal tail is found. As the pulvinar nucleus of the thalamus recedes superior to the hippocampus, the fornix will emerge.Finish editing the last coronal slice of the hippocampus in which the entire length of the fornix is visible, but not yet continuous with the splenium of the corpus callosum. Then, save the masks for both the left and right hippocampi in NifTI format. To construct a group template model load the shape modeling plug-in and click Open Directory to open a directory containing the binary masks of the study population of interest.Input the desired number of vertices and click Template Construction for the group template construction. Then check the mean shape mesh. For individual shape reconstruction, load the T1-weighted magnetic resonance image of interest and its corresponding segmentation mask and select the working directory to save the files.Select a template model for the individual shape modeling and check and modify the modeling parameters in the shape modeling plug-in as necessary. So our modeling framework is almost automated, however, some steps require user confirmation. For example, if the value for the hippocampal regions is not one users must change the intensity parameter.Then, check the result in the 3D view of the toolkit workbench. To perform a shape and deformity measurement select the shape model of the subject of interest in the data manager of the software and click Select Template to select the template of interest to obtain the measurement. Here, a representative deformation of the hippocampal template model for individual shape reconstruction can be observed.The method induces a large to small scale deformation of the template model to minimize the distortion of its point distribution while restoring the individual shape characteristics. In this figure, reconstructed shape models from two subjects with their segmentation masks are shown. In these images aligned individual shape models, their average model, and the shape difference vectors with an individual shape model can be observed.These data represent average shape deformity maps projected onto the average model. For one group with a small brain tissue volume, and one group with a large brain tissue volume. The shape deformity maps of the two groups present opposite patterns of hippocampal shape difference at corresponding regions.Check the segmentation mask and the individual or either the shared model together. If the model is not fitted to the image boundary, adjust the modeling parameters to achieve better results. Statistical analysis using the shape deformity can be performed to investigate the group-wise shape We have also provided MATLAB code for the analysis at our project page.This robust method has been applied to a number of clinical studies, not only involving critical structure modeling such as Alzheimer's disease or aging study, but also foot-bone disorders which require the analysis of compound bones.

Research

JoVE Journal

Neuroscience

Dissection and Culture of Mouse Dopaminergic and Striatal Explants in Three-Dimensional Collagen Matrix Assays

Midbrain dopamine (mdDA) neurons project via the medial forebrain bundle towards several areas in the telencephalon, including the striatum1. ...

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

After brain stroke microglia/macrophages (M/M) undergo  rapid activation with dramatic morphological and phenotypic changes that  include expression of ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Three-dimensional Imaging and Analysis of Mitochondria within Human Intraepidermal Nerve Fibers

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to ...

Peering at Brain Polysomes with Atomic Force Microscopy

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, ...

Anatomically Inspired Three-dimensional Micro-tissue Engineered Neural Networks for Nervous System Reconstruction, Modulation, and Modeling

Functional recovery rarely occurs&#160;following injury or disease-induced degeneration within the central nervous system (CNS)&#160;due to the inhibitory ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Chronic Implantation of Whole-cortical Electrocorticographic Array in the Common Marmoset

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent ...

Focused Ultrasound Induced Blood-Brain Barrier Opening for Targeting Brain Structures and Evaluating Chemogenetic Neuromodulation

Acoustically Targeted Chemogenetics (ATAC) allows for the noninvasive control of specific neural circuits. ATAC achieves such control through a ...

Three-Dimensional Motor Nerve Organoid Generation

A fascicle of axons is one of the major structural motifs observed in the nervous system. Disruption of axon fascicles could cause developmental and ...