Semi-automated generation of individual computational models of the human head and torso from MR images

Autor: Benjamin Kalloch, Arno Villringer, Mikhail Kozlov, André Pampel, Jens Bode, Mario Hlawitschka, Harald E. Möller, Bernhard Sehm, Pierre-Louis Bazin
Přispěvatelé: Netherlands Institute for Neuroscience (NIN), Spinoza Centre for Neuroimaging, Brain and Cognition, Brein en Cognitie (Psychologie, FMG)
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Adult
Male
Computer science
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
computer.software_genre
030218 nuclear medicine & medical imaging
Pattern Recognition
Automated
03 medical and health sciences
Young Adult
0302 clinical medicine
Electromagnetic Fields
Voxel
medicine
Image Processing
Computer-Assisted
Journal Article
Humans
Radiology
Nuclear Medicine and imaging
Computer vision
Segmentation
Computer Simulation
Gray Matter
Cerebrospinal Fluid
Skin
Human head
business.industry
Phantoms
Imaging
Skull
Brain
Torso
Image segmentation
Pipeline (software)
Magnetic Resonance Imaging
White Matter
Healthy Volunteers
Simulation software
medicine.anatomical_structure
Spinal Cord
Mesh generation
Programming Languages
Artificial intelligence
business
computer
Head
030217 neurology & neurosurgery
Algorithms
Software
Zdroj: Magnetic Resonance in Medicine, 81, 2090-2105. John Wiley and Sons Inc.
Magnetic Resonance in Medicine
Magnetic Resonance in Medicine, 81(3), 2090-2105. John Wiley and Sons Inc.
ISSN: 0740-3194
Popis: Purpose: Simulating the interaction of the human body with electromagnetic fields is an active field of research. Individualized models are increasingly being used, as anatomical differences affect the simulation results. We introduce a processing pipeline for creating individual surface-based models of the human head and torso for application in simulation software based on unstructured grids. The pipeline is designed for easy applicability and is publicly released on figshare. Methods: The pipeline covers image acquisition, segmentation, generation of segmentation masks, and surface mesh generation of the single, external boundary of each structure of interest. Two gradient-echo sequences are used for image acquisition. Structures of the head and body are segmented using several atlas-based approaches. They consist of bone/skull, subarachnoid cerebrospinal fluid, gray matter, white matter, spinal cord, lungs, the sinuses of the skull, and a combined class of all other structures including skin. After minor manual preparation, segmentation images are processed to segmentation masks, which are binarized images per segmented structure free of misclassified voxels and without an internal boundary. The proposed workflow is applied to 2 healthy subjects. Results: Individual differences of the subjects are well represented. The models are proven to be suitable for simulation of the RF electromagnetic field distribution. Conclusion: Image segmentation, creation of segmentation masks, and surface mesh generation are highly automated. Manual interventions remain for preparing the segmentation images prior to segmentation mask generation. The generated surfaces exhibit a single boundary per structure and are suitable inputs for simulation software.
Databáze: OpenAIRE
Externí odkaz: