An artificial immune-activated neural network applied to brain 3D MRI segmentation

An Automatic Parameter Decision System of Bilateral Filtering with GPU-Based Acceleration for Brain MR Images

Bilateral filters have been extensively utilized in a number of image denoising applications such as segmentation, registration, and tissue classification. However, it requires burdensome adjustments of the filter parameters to achieve the best performance for each individual image. To address this problem, this paper proposes a computer-aided parameter decision system based on image texture features associated with neural networks. In our approach, parallel computing with the GPU architecture is first developed to accelerate the computation of the conventional bilateral filter. Subsequently, a back propagation network (BPN) scheme using significant image texture features as the input is established to estimate the GPU-based bilateral filter parameters and its denoising process. The k-fold cross validation method is exploited to evaluate the performance of the proposed automatic restoration framework. A wide variety of T1-weighted brain MR images were employed to train and evaluate this parameter-free decision system with GPU-based bilateral filtering, which resulted in a speed-up factor of 208 comparing to the CPU-based computation. The proposed filter parameter prediction system achieved a mean absolute percentage error (MAPE) of 6% and was classified as "high accuracy". Our automatic denoising framework dramatically removed noise in numerous brain MR images and outperformed several state-of-the-art methods based on the peak signal-to-noise ratio (PSNR). The usage of image texture features associated with the BPN to estimate the GPU-based bilateral filter parameters and to automate the denoising process is feasible and validated. It is suggested that this automatic restoration system is advantageous to various brain MR image-processing applications.

Methods on Skull Stripping of MRI Head Scan Images-a Review

The high resolution magnetic resonance (MR) brain images contain some non-brain tissues such as skin, fat, muscle, neck, and eye balls compared to the functional images namely positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance imaging (fMRI) which usually contain relatively less non-brain tissues. The presence of these non-brain tissues is considered as a major obstacle for automatic brain image segmentation and analysis techniques. Therefore, quantitative morphometric studies of MR brain images often require a preliminary processing to isolate the brain from extra-cranial or non-brain tissues, commonly referred to as skull stripping. This paper describes the available methods on skull stripping and an exploratory review of recent literature on the existing skull stripping methods.

Accurate white matter lesion segmentation by k nearest neighbor classification with tissue type priors (kNN-TTPs)

Introduction

The segmentation and volumetric quantification of white matter (WM) lesions play an important role in monitoring and studying neurological diseases such as multiple sclerosis (MS) or cerebrovascular disease. This is often interactively done using 2D magnetic resonance images. Recent developments in acquisition techniques allow for 3D imaging with much thinner sections, but the large number of images per subject makes manual lesion outlining infeasible. This warrants the need for a reliable automated approach. Here we aimed to improve k nearest neighbor (kNN) classification of WM lesions by optimizing intensity normalization and using spatial tissue type priors (TTPs).

Methods

The kNN-TTP method used kNN classification with 3.0 T 3DFLAIR and 3DT1 intensities as well as MNI-normalized spatial coordinates as features. Additionally, TTPs were computed by nonlinear registration of data from healthy controls. Intensity features were normalized using variance scaling, robust range normalization or histogram matching. The algorithm was then trained and evaluated using a leave-one-out experiment among 20 patients with MS against a reference segmentation that was created completely manually. The performance of each normalization method was evaluated both with and without TTPs in the feature set. Volumetric agreement was evaluated using intra-class coefficient (ICC), and voxelwise spatial agreement was evaluated using Dice similarity index (SI). Finally, the robustness of the method across different scanners and patient populations was evaluated using an independent sample of elderly subjects with hypertension.

Results

The intensity normalization method had a large influence on the segmentation performance, with average SI values ranging from 0.66 to 0.72 when no TTPs were used. Independent of the normalization method, the inclusion of TTPs as features increased performance particularly by reducing the lesion detection error. Best performance was achieved using variance scaled intensity features and including TTPs in the feature set: this yielded ICC = 0.93 and average SI = 0.75 ± 0.08. Validation of the method in an independent sample of elderly subjects with hypertension, yielded even higher ICC = 0.96 and SI = 0.84 ± 0.14.

Conclusion

Adding TTPs increases the performance of kNN based MS lesion segmentation methods. Best performance was achieved using variance scaling for intensity normalization and including TTPs in the feature set, showing excellent agreement with the reference segmentations across a wide range of lesion severity, irrespective of the scanner used or the pathological substrate of the lesions.

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Intensity normalization has a large influence on lesion segmentation performance.

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Inclusion of tissue type priors as features increases segmentation performance.

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Best performance was achieved using variance scaling and tissue type priors.

Multi-Sectional Views Textural Based SVM for MS Lesion Segmentation in Multi-Channels MRIs

In this paper, a new technique is proposed for automatic segmentation of multiple sclerosis (MS) lesions from brain magnetic resonance imaging (MRI) data. The technique uses a trained support vector machine (SVM) to discriminate between the blocks in regions of MS lesions and the blocks in non-MS lesion regions mainly based on the textural features with aid of the other features. The classification is done on each of the axial, sagittal and coronal sectional brain view independently and the resultant segmentations are aggregated to provide more accurate output segmentation. The main contribution of the proposed technique described in this paper is the use of textural features to detect MS lesions in a fully automated approach that does not rely on manually delineating the MS lesions. In addition, the technique introduces the concept of the multi-sectional view segmentation to produce verified segmentation. The proposed textural-based SVM technique was evaluated using three simulated datasets and more than fifty real MRI datasets. The results were compared with state of the art methods. The obtained results indicate that the proposed method would be viable for use in clinical practice for the detection of MS lesions in MRI.

Multi-Sectional Views Textural Based SVM for MS Lesion Segmentation in Multi-Channels MRIs

In this paper, a new technique is proposed for automatic segmentation of multiple sclerosis (MS) lesions from brain magnetic resonance imaging (MRI) data. The technique uses a trained support vector machine (SVM) to discriminate between the blocks in regions of MS lesions and the blocks in non-MS lesion regions mainly based on the textural features with aid of the other features. The classification is done on each of the axial, sagittal and coronal sectional brain view independently and the resultant segmentations are aggregated to provide more accurate output segmentation. The main contribution of the proposed technique described in this paper is the use of textural features to detect MS lesions in a fully automated approach that does not rely on manually delineating the MS lesions. In addition, the technique introduces the concept of the multi-sectional view segmentation to produce verified segmentation. The proposed textural-based SVM technique was evaluated using three simulated datasets and more than fifty real MRI datasets. The results were compared with state of the art methods. The obtained results indicate that the proposed method would be viable for use in clinical practice for the detection of MS lesions in MRI.