Design and construction of a realistic digital brain phantom
TL;DR: The authors present a realistic, high-resolution, digital, volumetric phantom of the human brain, which can be used to simulate tomographic images of the head and is the ideal tool to test intermodality registration algorithms.
Abstract: After conception and implementation of any new medical image processing algorithm, validation is an important step to ensure that the procedure fulfils all requirements set forth at the initial design stage. Although the algorithm must be evaluated on real data, a comprehensive validation requires the additional use of simulated data since it is impossible to establish ground truth with in vivo data. Experiments with simulated data permit controlled evaluation over a wide range of conditions (e.g., different levels of noise, contrast, intensity artefacts, or geometric distortion). Such considerations have become increasingly important with the rapid growth of neuroimaging, i.e., computational analysis of brain structure and function using brain scanning methods such as positron emission tomography and magnetic resonance imaging. Since simple objects such as ellipsoids or parallelepipedes do not reflect the complexity of natural brain anatomy, the authors present the design and creation of a realistic, high-resolution, digital, volumetric phantom of the human brain. This three-dimensional digital brain phantom is made up of ten volumetric data sets that define the spatial distribution for different tissues (e.g., grey matter, white matter, muscle, skin, etc.), where voxel intensity is proportional to the fraction of tissue within the voxel. The digital brain phantom can be used to simulate tomographic images of the head. Since the contribution of each tissue type to each voxel in the brain phantom is known, it can be used as the gold standard to test analysis algorithms such as classification procedures which seek to identify the tissue "type" of each image voxel. Furthermore, since the same anatomical phantom may be used to drive simulators for different modalities, it is the ideal tool to test intermodality registration algorithms. The brain phantom and simulated MR images have been made publicly available on the Internet (http://www.bic.mni.mcgill.ca/brainweb).
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TL;DR: An anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute was performed and it is believed that this tool is an improvement for the macroscopical labeling of activated area compared to labeling assessed using the Talairach atlas brain.
13,678 citations
TL;DR: In this paper, the authors describe the steps involved in VBM, with particular emphasis on segmenting gray matter from MR images with non-uniformity artifact and provide evaluations of the assumptions that underpin the method, including the accuracy of the segmentation and the assumptions made about the statistical distribution of the data.
8,049 citations
TL;DR: A look at progress in the field over the last 20 years is looked at and some of the challenges that remain for the years to come are suggested.
Abstract: The analysis of medical images has been woven into the fabric of the pattern analysis and machine intelligence (PAMI) community since the earliest days of these Transactions. Initially, the efforts in this area were seen as applying pattern analysis and computer vision techniques to another interesting dataset. However, over the last two to three decades, the unique nature of the problems presented within this area of study have led to the development of a new discipline in its own right. Examples of these include: the types of image information that are acquired, the fully three-dimensional image data, the nonrigid nature of object motion and deformation, and the statistical variation of both the underlying normal and abnormal ground truth. In this paper, we look at progress in the field over the last 20 years and suggest some of the challenges that remain for the years to come.
4,249 citations
TL;DR: A variant of the popular nonparametric nonuniform intensity normalization (N3) algorithm is proposed for bias field correction with the substitution of a recently developed fast and robust B-spline approximation routine and a modified hierarchical optimization scheme for improved bias field Correction over the original N3 algorithm.
Abstract: A variant of the popular nonparametric nonuniform intensity normalization (N3) algorithm is proposed for bias field correction. Given the superb performance of N3 and its public availability, it has been the subject of several evaluation studies. These studies have demonstrated the importance of certain parameters associated with the B-spline least-squares fitting. We propose the substitution of a recently developed fast and robust B-spline approximation routine and a modified hierarchical optimization scheme for improved bias field correction over the original N3 algorithm. Similar to the N3 algorithm, we also make the source code, testing, and technical documentation of our contribution, which we denote as ?N4ITK,? available to the public through the Insight Toolkit of the National Institutes of Health. Performance assessment is demonstrated using simulated data from the publicly available Brainweb database, hyperpolarized 3He lung image data, and 9.4T postmortem hippocampus data.
4,090 citations
Cites methods from "Design and construction of a realis..."
...A component of the evaluation in [5] involved comparing known bias fields with the extracted bias fields produced by the six bias correction algorithms being studied using the Brainweb database [24]–[26]....
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TL;DR: Brainstorm as discussed by the authors is a collaborative open-source application dedicated to magnetoencephalography (MEG) and EEG data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data.
Abstract: Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI).
2,637 citations
References
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Book•
31 Jul 1981
TL;DR: Books, as a source that may involve the facts, opinion, literature, religion, and many others are the great friends to join with, becomes what you need to get.
Abstract: New updated! The latest book from a very famous author finally comes out. Book of pattern recognition with fuzzy objective function algorithms, as an amazing reference becomes what you need to get. What's for is this book? Are you still thinking for what the book is? Well, this is what you probably will get. You should have made proper choices for your better life. Book, as a source that may involve the facts, opinion, literature, religion, and many others are the great friends to join with.
15,662 citations
"Design and construction of a realis..." refers methods in this paper
...(The “ ” differentiates volumes output from the classifier from those finally used to build the phantom after manual correction.) These training points were used to drive four different automatic classification procedures [19]: minimum-distance, nearest K-mean, fuzzy C-mean [ 20 ], and artificial neural network (ANN) [21]....
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Book•
01 Jan 1988
TL;DR: Direct and Indirect Radiologic Localization Reference System: Basal Brain Line CA-CP Cerebral Structures in Three-Dimensional Space Practical Examples for the Use of the Atlas in Neuroradiologic Examinations Three- Dimensional Atlas of a Human Brain Nomenclature-Abbreviations Anatomic Index Conclusions.
Abstract: Direct and Indirect Radiologic Localization Reference System: Basal Brain Line CA-CP Cerebral Structures in Three-Dimensional Space Practical Examples for the Use of the Atlas in Neuroradiologic Examinations Three-Dimensional Atlas of a Human Brain Nomenclature-Abbreviations Anatomic Index Conclusions.
9,491 citations
TL;DR: A novel approach to correcting for intensity nonuniformity in magnetic resonance (MR) data is described that achieves high performance without requiring a model of the tissue classes present, and is applied at an early stage in an automated data analysis, before a tissue model is available.
Abstract: A novel approach to correcting for intensity nonuniformity in magnetic resonance (MR) data is described that achieves high performance without requiring a model of the tissue classes present. The method has the advantage that it can be applied at an early stage in an automated data analysis, before a tissue model is available. Described as nonparametric nonuniform intensity normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. The performance of this method is evaluated using both real and simulated MR data.
4,613 citations
Additional excerpts
...the intensity histogram of the image [18]....
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TL;DR: A fully automatic registration method to map volumetric data into stereotaxic space that yields results comparable with those of manually based techniques and therefore does not suffer the drawbacks involved in user intervention.
Abstract: Objective In both diagnostic and research applications, the interpretation of MR images of the human brain is facilitated when different data sets can be compared by visual inspection of equivalent anatomical planes. Quantitative analysis with predefined atlas templates often requires the initial alignment of atlas and image planes. Unfortunately, the axial planes acquired during separate scanning sessions are often different in their relative position and orientation, and these slices are not coplanar with those in the atlas. We have developed a completely automatic method to register a given volumetric data set with Talairach stereotaxic coordinate system. Materials and methods The registration method is based on multi-scale, three-dimensional (3D) cross-correlation with an average (n > 300) MR brain image volume aligned with the Talariach stereotaxic space. Once the data set is re-sampled by the transformation recovered by the algorithm, atlas slices can be directly superimposed on the corresponding slices of the re-sampled volume. the use of such a standardized space also allows the direct comparison, voxel to voxel, of two or more data sets brought into stereotaxic space. Results With use of a two-tailed Student t test for paired samples, there was no significant difference in the transformation parameters recovered by the automatic algorithm when compared with two manual landmark-based methods (p > 0.1 for all parameters except y-scale, where p > 0.05). Using root-mean-square difference between normalized voxel intensities as an unbiased measure of registration, we show that when estimated and averaged over 60 volumetric MR images in standard space, this measure was 30% lower for the automatic technique than the manual method, indicating better registrations. Likewise, the automatic method showed a 57% reduction in standard deviation, implying a more stable technique. The algorithm is able to recover the transformation even when data are missing from the top or bottom of the volume. Conclusion We present a fully automatic registration method to map volumetric data into stereotaxic space that yields results comparable with those of manually based techniques. The method requires no manual identification of points or contours and therefore does not suffer the drawbacks involved in user intervention such as reproducibility and interobserver variability.
3,357 citations
"Design and construction of a realis..." refers methods in this paper
...It is used widely for intrasubject and intersubject image alignment, comparison and quantitative analysis [16], [ 17 ]....
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Book•
01 Jan 1992
TL;DR: Jacek M. Zurada is a Professor with the Electrical and Computer Engineering Department at the University of Louisville, Kentucky and has published over 350 journal and conference papers in the areas of neural networks, computational intelligence, data mining, image processing and VLSI circuits.
Abstract: Jacek M. Zurada received his MS and Ph.D. degrees (with distinction) in electrical engineering from the Technical University of Gdansk, Poland. Since 1989 he has been a Professor with the Electrical and Computer Engineering Department at the University of Louisville, Kentucky. He was Department Chair from 2004 to 2006. He has published over 350 journal and conference papers in the areas of neural networks, computational intelligence, data mining, image processing and VLSI circuits. INTRODUCTION TO ARTIFICIAL NEURAL SYSTEMS
2,883 citations
"Design and construction of a realis..." refers methods in this paper
...(The “ ” differentiates volumes output from the classifier from those finally used to build the phantom after manual correction.) These training points were used to drive four different automatic classification procedures [19]: minimum-distance, nearest K-mean, fuzzy C-mean [20], and artificial neural network (ANN) [ 21 ]....
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