17,498 research outputs found
A Three-dimensional Deformable Brain Atlas for DBS Targeting. I. Methodology for Atlas Creation and Artifact Reduction.
BackgroundTargeting in deep brain stimulation (DBS) relies heavily on the ability to accurately localize particular anatomic brain structures. Direct targeting of subcortical structures has been limited by the ability to visualize relevant DBS targets.Methods and resultsIn this work, we describe the development and implementation, of a methodology utilized to create a three dimensional deformable atlas for DBS surgery. This atlas was designed to correspond to the print version of the Schaltenbrand-Bailey atlas structural contours. We employed a smoothing technique to reduce artifacts inherent in the print version.ConclusionsWe present the methodology used to create a three dimensional patient specific DBS atlas which may in the future be tested for clinical utility
Feature Lines for Illustrating Medical Surface Models: Mathematical Background and Survey
This paper provides a tutorial and survey for a specific kind of illustrative
visualization technique: feature lines. We examine different feature line
methods. For this, we provide the differential geometry behind these concepts
and adapt this mathematical field to the discrete differential geometry. All
discrete differential geometry terms are explained for triangulated surface
meshes. These utilities serve as basis for the feature line methods. We provide
the reader with all knowledge to re-implement every feature line method.
Furthermore, we summarize the methods and suggest a guideline for which kind of
surface which feature line algorithm is best suited. Our work is motivated by,
but not restricted to, medical and biological surface models.Comment: 33 page
Anatomical landmark based registration of contrast enhanced T1-weighted MR images
In many problems involving multiple image analysis, an im- age registration step is required. One such problem appears in brain tumor imaging, where baseline and follow-up image volumes from a tu- mor patient are often to-be compared. Nature of the registration for a change detection problem in brain tumor growth analysis is usually rigid or affine. Contrast enhanced T1-weighted MR images are widely used in clinical practice for monitoring brain tumors. Over this modality, con- tours of the active tumor cells and whole tumor borders and margins are visually enhanced. In this study, a new technique to register serial contrast enhanced T1 weighted MR images is presented. The proposed fully-automated method is based on five anatomical landmarks: eye balls, nose, confluence of sagittal sinus, and apex of superior sagittal sinus. Af- ter extraction of anatomical landmarks from fixed and moving volumes, an affine transformation is estimated by minimizing the sum of squared distances between the landmark coordinates. Final result is refined with a surface registration, which is based on head masks confined to the sur- face of the scalp, as well as to a plane constructed from three of the extracted features. The overall registration is not intensity based, and it depends only on the invariant structures. Validation studies using both synthetically transformed MRI data, and real MRI scans, which included several markers over the head of the patient were performed. In addition, comparison studies against manual landmarks marked by a radiologist, as well as against the results obtained from a typical mutual information based method were carried out to demonstrate the effectiveness of the proposed method
Single-image Tomography: 3D Volumes from 2D Cranial X-Rays
As many different 3D volumes could produce the same 2D x-ray image, inverting
this process is challenging. We show that recent deep learning-based
convolutional neural networks can solve this task. As the main challenge in
learning is the sheer amount of data created when extending the 2D image into a
3D volume, we suggest firstly to learn a coarse, fixed-resolution volume which
is then fused in a second step with the input x-ray into a high-resolution
volume. To train and validate our approach we introduce a new dataset that
comprises of close to half a million computer-simulated 2D x-ray images of 3D
volumes scanned from 175 mammalian species. Applications of our approach
include stereoscopic rendering of legacy x-ray images, re-rendering of x-rays
including changes of illumination, view pose or geometry. Our evaluation
includes comparison to previous tomography work, previous learning methods
using our data, a user study and application to a set of real x-rays
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
Image and Volume Segmentation by Water Flow
A general framework for image segmentation is presented in this paper, based on the paradigm of water flow. The major water flow attributes like water pressure, surface tension and capillary force are defined in the context of force field generation and make the model adaptable to topological and geometrical changes. A flow-stopping image functional combining edge- and region-based forces is introduced to produce capability for both range and accuracy. The method is assessed qualitatively and quantitatively on synthetic and natural images. It is shown that the new approach can segment objects with complex shapes or weak-contrasted boundaries, and has good immunity to noise. The operator is also extended to 3-D, and is successfully applied to medical volume segmentation
From Multiview Image Curves to 3D Drawings
Reconstructing 3D scenes from multiple views has made impressive strides in
recent years, chiefly by correlating isolated feature points, intensity
patterns, or curvilinear structures. In the general setting - without
controlled acquisition, abundant texture, curves and surfaces following
specific models or limiting scene complexity - most methods produce unorganized
point clouds, meshes, or voxel representations, with some exceptions producing
unorganized clouds of 3D curve fragments. Ideally, many applications require
structured representations of curves, surfaces and their spatial relationships.
This paper presents a step in this direction by formulating an approach that
combines 2D image curves into a collection of 3D curves, with topological
connectivity between them represented as a 3D graph. This results in a 3D
drawing, which is complementary to surface representations in the same sense as
a 3D scaffold complements a tent taut over it. We evaluate our results against
truth on synthetic and real datasets.Comment: Expanded ECCV 2016 version with tweaked figures and including an
overview of the supplementary material available at
multiview-3d-drawing.sourceforge.ne
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