826 research outputs found
Brain Tumor Detection and Segmentation in Multisequence MRI
Tato prĂĄce se zabĂœvĂĄ detekcĂ a segmentacĂ mozkovĂ©ho nĂĄdoru v multisekvenÄnĂch MR obrazech se zamÄĆenĂm na gliomy vysokĂ©ho a nĂzkĂ©ho stupnÄ malignity. Jsou zde pro tento ĂșÄel navrĆŸeny tĆi metody. PrvnĂ metoda se zabĂœvĂĄ detekcĂ prezence ÄĂĄstĂ mozkovĂ©ho nĂĄdoru v axiĂĄlnĂch a koronĂĄrnĂch Ćezech. JednĂĄ se o algoritmus zaloĆŸenĂœ na analĂœze symetrie pĆi rĆŻznĂœch rozliĆĄenĂch obrazu, kterĂœ byl otestovĂĄn na T1, T2, T1C a FLAIR obrazech. DruhĂĄ metoda se zabĂœvĂĄ extrakcĂ oblasti celĂ©ho mozkovĂ©ho nĂĄdoru, zahrnujĂcĂ oblast jĂĄdra tumoru a edĂ©mu, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkovĂœ nĂĄdor z 2D i 3D obrazĆŻ. Je zde opÄt vyuĆŸita analĂœza symetrie, kterĂĄ je nĂĄsledovĂĄna automatickĂœm stanovenĂm intenzitnĂho prahu z nejvĂce asymetrickĂœch ÄĂĄstĂ. TĆetĂ metoda je zaloĆŸena na predikci lokĂĄlnĂ struktury a je schopna segmentovat celou oblast nĂĄdoru, jeho jĂĄdro i jeho aktivnĂ ÄĂĄst. Metoda vyuĆŸĂvĂĄ faktu, ĆŸe vÄtĆĄina lĂ©kaĆskĂœch obrazĆŻ vykazuje vysokou podobnost intenzit sousednĂch pixelĆŻ a silnou korelaci mezi intenzitami v rĆŻznĂœch obrazovĂœch modalitĂĄch. JednĂm ze zpĆŻsobĆŻ, jak s touto korelacĂ pracovat a pouĆŸĂvat ji, je vyuĆŸitĂ lokĂĄlnĂch obrazovĂœch polĂ. PodobnĂĄ korelace existuje takĂ© mezi sousednĂmi pixely v anotaci obrazu. Tento pĆĂznak byl vyuĆŸit v predikci lokĂĄlnĂ struktury pĆi lokĂĄlnĂ anotaci polĂ. Jako klasifikaÄnĂ algoritmus je v tĂ©to metodÄ pouĆŸita konvoluÄnĂ neuronovĂĄ sĂĆ„ vzhledem k jejĂ znĂĄme schopnosti zachĂĄzet s korelacĂ mezi pĆĂznaky. VĆĄechny tĆi metody byly otestovĂĄny na veĆejnĂ© databĂĄzi 254 multisekvenÄnĂch MR obrazech a byla dosĂĄhnuta pĆesnost srovnatelnĂĄ s nejmodernÄjĆĄĂmi metodami v mnohem kratĆĄĂm vĂœpoÄetnĂm Äase (v ĆĂĄdu sekund pĆi pouĆŸitĂœ CPU), coĆŸ poskytuje moĆŸnost manuĂĄlnĂch Ășprav pĆi interaktivnĂ segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.
Improvements in the registration of multimodal medical imaging : application to intensity inhomogeneity and partial volume corrections
Alignment or registration of medical images has a relevant role on clinical diagnostic and treatment decisions as well as in research settings. With the advent of new technologies for multimodal imaging, robust registration of functional and anatomical information is still a challenge, particular in small-animal imaging given the lesser structural content of certain anatomical parts, such as the brain, than in humans. Besides, patient-dependent and acquisition artefacts affecting the images information content further complicate registration, as is the case of intensity inhomogeneities (IIH) showing in MRI and the partial volume effect (PVE) attached to PET imaging. Reference methods exist for accurate image registration but their performance is severely deteriorated in situations involving little images Overlap. While several approaches to IIH and PVE correction exist these methods still do not guarantee or rely on robust registration. This Thesis focuses on overcoming current limitations af registration to enable novel IIH and PVE correction methods.El registre d'imatges mĂšdiques tĂ© un paper rellevant en les decisions de diagnĂČstic i tractament clĂniques aixĂ com en la recerca. Amb el desenvolupament de noves tecnologies d'imatge multimodal, el registre robust d'informaciĂł funcional i anatĂČmica Ă©s encara avui un repte, en particular, en imatge de petit animal amb un menor contingut estructural que en humans de certes parts anatĂČmiques com el cervell. A mĂ©s, els artefactes induĂŻts pel propi pacient i per la tĂšcnica d'adquisiciĂł que afecten el contingut d'informaciĂł de les imatges complica encara mĂ©s el procĂ©s de registre. Ăs el cas de les inhomogeneĂŻtats d'intensitat (IIH) que apareixen a les RM i de l'efecte de volum parcial (PVE) caracterĂstic en PET. Tot i que existeixen mĂštodes de referĂšncia pel registre acurat d'imatges la seva eficĂ cia es veu greument minvada en casos de poc solapament entre les imatges. De la mateixa manera, tambĂ© existeixen mĂštodes per la correcciĂł d'IIH i de PVE perĂČ que no garanteixen o que requereixen un registre robust. Aquesta tesi es centra en superar aquestes limitacions sobre el registre per habilitar nous mĂštodes per la correcciĂł d'IIH i de PVE
Medical Image Segmentation Based on Multi-Modal Convolutional Neural Network: Study on Image Fusion Schemes
Image analysis using more than one modality (i.e. multi-modal) has been
increasingly applied in the field of biomedical imaging. One of the challenges
in performing the multimodal analysis is that there exist multiple schemes for
fusing the information from different modalities, where such schemes are
application-dependent and lack a unified framework to guide their designs. In
this work we firstly propose a conceptual architecture for the image fusion
schemes in supervised biomedical image analysis: fusing at the feature level,
fusing at the classifier level, and fusing at the decision-making level.
Further, motivated by the recent success in applying deep learning for natural
image analysis, we implement the three image fusion schemes above based on the
Convolutional Neural Network (CNN) with varied structures, and combined into a
single framework. The proposed image segmentation framework is capable of
analyzing the multi-modality images using different fusing schemes
simultaneously. The framework is applied to detect the presence of soft tissue
sarcoma from the combination of Magnetic Resonance Imaging (MRI), Computed
Tomography (CT) and Positron Emission Tomography (PET) images. It is found from
the results that while all the fusion schemes outperform the single-modality
schemes, fusing at the feature level can generally achieve the best performance
in terms of both accuracy and computational cost, but also suffers from the
decreased robustness in the presence of large errors in any image modalities.Comment: Zhe Guo and Xiang Li contribute equally to this wor
Wavelet Features for Recognition of First Episode of Schizophrenia from MRI Brain Images
Machine learning methods are increasingly used in various fields of medicine, contributing to early diagnosis and better quality of care. These outputs are particularly desirable in case of neuropsychiatric disorders, such as schizophrenia, due to the inherent potential for creating a new gold standard in the diagnosis and differentiation of particular disorders. This paper presents a scheme for automated classification from magnetic resonance images based on multiresolution representation in the wavelet domain. Implementation of the proposed algorithm, utilizing support vector machines classifier, is introduced and tested on a dataset containing 104 patients with first episode schizophrenia and healthy volunteers. Optimal parameters of different phases of the algorithm are sought and the quality of classification is estimated by robust cross validation techniques. Values of accuracy, sensitivity and specificity over 71% are achieved
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Deep learning assisted MRI guided attenuation correction in PET
This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological
and functional details of the tissue at the molecular level. However, the acquired PET images
have some limitations such as the attenuation. PET attenuation correction is an essential step to
obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners,
magnetic resonance (MR) images are used to address the problem of PET attenuation correction.
The MR images segmentation is one simple and robust approach to create pseudo computed
tomography (CT) images, which are used to generate attenuation coefficient maps to correct the
PET attenuation. Recently, deep learning has been proposed and used as a promising technique
to efficiently perform MR and various medical images segmentation.
In this research work, deep learning guided segmentation approaches have been proposed
to enhance the bone class segmentation of MR brain images in order to generate accurate
pseudo-CT images. The first approach has introduced the combination of handcrafted features
with deep learning features to enrich the set of features. Multiresolution analysis techniques,
which generate multiscale and multidirectional coefficients of an image such as contourlet and
shearlet transforms, are applied and combined with deep convolutional neural network (CNN)
features. Different experiments have been conducted to investigate the number of selected
coefficients and the insertion location of the handcrafted features.
The second approach aims at reducing the segmentation algorithmâs complexity while
maintaining the segmentation performance. An attention based convolutional encode-decoder
network has been proposed to adaptively recalibrate the deep network features. This attention based
network consists of two different squeeze and excitation blocks that excite the features
spatially and channel wise. The two blocks are combined sequentially to decrease the number
of networkâs parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A
pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w
images. Multiple fine tuning approaches and experiments have been conducted to study the best
fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and
T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been
used to carry an objective evaluation to measure the segmentation performance of the results
obtained by the three proposed methods. The first and second approaches have been validated
with other studies in the literature that applied deep network based segmentation technique to
perform MR based attenuation correction for PET images. The proposed methods have shown
an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC)
from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%.
The proposed excitation-based CNN has decreased the model complexity by decreasing the
number of trainable parameters by more than 46% where less computing resources are required
to train the model. The proposed hybrid transfer learning method has shown its superiority to
build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied
transfer learning methods especially with the bone class where the DSC is increased from 0.3841
to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than
transfer learning using open and conservative fine tuning
Bayesian Spatial Binary Regression for Label Fusion in Structural Neuroimaging
Many analyses of neuroimaging data involve studying one or more regions of
interest (ROIs) in a brain image. In order to do so, each ROI must first be
identified. Since every brain is unique, the location, size, and shape of each
ROI varies across subjects. Thus, each ROI in a brain image must either be
manually identified or (semi-) automatically delineated, a task referred to as
segmentation. Automatic segmentation often involves mapping a previously
manually segmented image to a new brain image and propagating the labels to
obtain an estimate of where each ROI is located in the new image. A more recent
approach to this problem is to propagate labels from multiple manually
segmented atlases and combine the results using a process known as label
fusion. To date, most label fusion algorithms either employ voting procedures
or impose prior structure and subsequently find the maximum a posteriori
estimator (i.e., the posterior mode) through optimization. We propose using a
fully Bayesian spatial regression model for label fusion that facilitates
direct incorporation of covariate information while making accessible the
entire posterior distribution. We discuss the implementation of our model via
Markov chain Monte Carlo and illustrate the procedure through both simulation
and application to segmentation of the hippocampus, an anatomical structure
known to be associated with Alzheimer's disease.Comment: 24 pages, 10 figure
AUTOMATIC 3D DEFORMED MIDSAGITTAL SURFACE LOCALIZATION BY CONSTRAINED MONTE CARLO OPTIMIZATION
AUTOMATIC 3D DEFORMED MIDSAGITTAL SURFACE LOCALIZATION BY CONSTRAINED MONTE CARLO OPTIMIZATIO
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