26,177 research outputs found
Introduction to fMRI: experimental design and data analysis
This provides an introduction to functional MRI, experimental design and data analysis procedures using statistical parametric mapping approach
Incorporating Relaxivities to More Accurately Reconstruct MR Images
Purpose
To develop a mathematical model that incorporates the magnetic resonance relaxivities into the image reconstruction process in a single step.
Materials and methods
In magnetic resonance imaging, the complex-valued measurements of the acquired signal at each point in frequency space are expressed as a Fourier transformation of the proton spin density weighted by Fourier encoding anomalies: T2â, T1, and a phase determined by magnetic field inhomogeneity (âB) according to the MR signal equation. Such anomalies alter the expected symmetry and the signal strength of the k-space observations, resulting in images distorted by image warping, blurring, and loss in image intensity. Although T1 on tissue relaxation time provides valuable quantitative information on tissue characteristics, the T1 recovery term is typically neglected by assuming a long repetition time. In this study, the linear framework presented in the work of Rowe et al., 2007, and of Nencka et al., 2009 is extended to develop a Fourier reconstruction operation in terms of a real-valued isomorphism that incorporates the effects of T2â, âB, and T1. This framework provides a way to precisely quantify the statistical properties of the corrected image-space data by offering a linear relationship between the observed frequency space measurements and reconstructed corrected image-space measurements. The model is illustrated both on theoretical data generated by considering T2â, T1, and/or âB effects, and on experimentally acquired fMRI data by focusing on the incorporation of T1. A comparison is also made between the activation statistics computed from the reconstructed data with and without the incorporation of T1 effects.
Result
Accounting for T1 effects in image reconstruction is shown to recover image contrast that exists prior to T1 equilibrium. The incorporation of T1 is also shown to induce negligible correlation in reconstructed images and preserve functional activations.
Conclusion
With the use of the proposed method, the effects of T2â and âB can be corrected, and T1 can be incorporated into the time series image-space data during image reconstruction in a single step. Incorporation of T1 provides improved tissue segmentation over the course of time series and therefore can improve the precision of motion correction and image registration
Simultaneous in vivo positron emission tomography and magnetic resonance imaging
Positron emission tomography (PET) and magnetic resonance imaging (MRI) are widely used in vivo imaging technologies with both clinical and biomedical research applications. The strengths of MRI include high-resolution, high-contrast morphologic imaging of soft tissues; the ability to image physiologic parameters such as diffusion and changes in oxygenation level resulting from neuronal stimulation; and the measurement of metabolites using chemical shift imaging. PET images the distribution of biologically targeted radiotracers with high sensitivity, but images generally lack anatomic context and are of lower spatial resolution. Integration of these technologies permits the acquisition of temporally correlated data showing the distribution of PET radiotracers and MRI contrast agents or MR-detectable metabolites, with registration to the underlying anatomy. An MRI-compatible PET scanner has been built for biomedical research applications that allows data from both modalities to be acquired simultaneously. Experiments demonstrate no effect of the MRI system on the spatial resolution of the PET system and <10% reduction in the fraction of radioactive decay events detected by the PET scanner inside the MRI. The signal-to-noise ratio and uniformity of the MR images, with the exception of one particular pulse sequence, were little affected by the presence of the PET scanner. In vivo simultaneous PET and MRI studies were performed in mice. Proof-of-principle in vivo MR spectroscopy and functional MRI experiments were also demonstrated with the combined scanner
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Prediction of Treatment Response to Neoadjuvant Chemotherapy for Breast Cancer via Early Changes in Tumor Heterogeneity Captured by DCE-MRI Registration.
We analyzed DCE-MR images from 132 women with locally advanced breast cancer from the I-SPY1 trial to evaluate changes of intra-tumor heterogeneity for augmenting early prediction of pathologic complete response (pCR) and recurrence-free survival (RFS) after neoadjuvant chemotherapy (NAC). Utilizing image registration, voxel-wise changes including tumor deformations and changes in DCE-MRI kinetic features were computed to characterize heterogeneous changes within the tumor. Using five-fold cross-validation, logistic regression and Cox regression were performed to model pCR and RFS, respectively. The extracted imaging features were evaluated in augmenting established predictors, including functional tumor volume (FTV) and histopathologic and demographic factors, using the area under the curve (AUC) and the C-statistic as performance measures. The extracted voxel-wise features were also compared to analogous conventional aggregated features to evaluate the potential advantage of voxel-wise analysis. Voxel-wise features improved prediction of pCR (AUCâ=â0.78 (±0.03) vs 0.71 (±0.04), pâ<â0.05 and RFS (C-statisticâ=â0.76 (â±â0.05), vs 0.63 (â±â0.01)), pâ<â0.05, while models based on analogous aggregate imaging features did not show appreciable performance changes (pâ>â0.05). Furthermore, all selected voxel-wise features demonstrated significant association with outcome (pâ<â0.05). Thus, precise measures of voxel-wise changes in tumor heterogeneity extracted from registered DCE-MRI scans can improve early prediction of neoadjuvant treatment outcomes in locally advanced breast cancer
The Integration of Positron Emission Tomography With Magnetic Resonance Imaging
A number of laboratories and companies are currently exploring the development of integrated imaging systems for magnetic resonance imaging (MRI) and positron emission tomography (PET). Scanners for both preclinical and human research applications are being pursued. In contrast to the widely distributed and now quite mature PET/computed tomography technology, most PET/MRI designs allow for simultaneous rather than sequential acquisition of PET and MRI data. While this offers the possibility of novel imaging strategies, it also creates considerable challenges for acquiring artifact-free images from both modalities. This paper discusses the motivation for developing combined PET/MRI technology, outlines the obstacles in realizing such an integrated instrument, and presents recent progress in the development of both the instrumentation and of novel imaging agents for combined PET/MRI studies. The performance of the first-generation PET/MRI systems is described. Finally, a range of possible biomedical applications for PET/MRI are outlined
Microtesla MRI of the human brain combined with MEG
One of the challenges in functional brain imaging is integration of
complementary imaging modalities, such as magnetoencephalography (MEG) and
functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive
superconducting quantum interference devices (SQUIDs) to directly measure
magnetic fields of neuronal currents, cannot be combined with conventional
high-field MRI in a single instrument. Indirect matching of MEG and MRI data
leads to significant co-registration errors. A recently proposed imaging method
- SQUID-based microtesla MRI - can be naturally combined with MEG in the same
system to directly provide structural maps for MEG-localized sources. It
enables easy and accurate integration of MEG and MRI/fMRI, because microtesla
MR images can be precisely matched to structural images provided by high-field
MRI and other techniques. Here we report the first images of the human brain by
microtesla MRI, together with auditory MEG (functional) data, recorded using
the same seven-channel SQUID system during the same imaging session. The images
were acquired at 46 microtesla measurement field with pre-polarization at 30
mT. We also estimated transverse relaxation times for different tissues at
microtesla fields. Our results demonstrate feasibility and potential of human
brain imaging by microtesla MRI. They also show that two new types of imaging
equipment - low-cost systems for anatomical MRI of the human brain at
microtesla fields, and more advanced instruments for combined functional (MEG)
and structural (microtesla MRI) brain imaging - are practical.Comment: 8 pages, 5 figures - accepted by JM
Breast Cancer: Modelling and Detection
This paper reviews a number of the mathematical models used in cancer modelling and then chooses a specific cancer, breast carcinoma, to illustrate how the modelling can be used in aiding detection. We then discuss mathematical models that underpin mammographic image analysis, which complements models of tumour growth and facilitates diagnosis and treatment of cancer. Mammographic images are notoriously difficult to interpret, and we give an overview of the primary image enhancement technologies that have been introduced, before focusing on a more detailed description of some of our own recent work on the use of physics-based modelling in mammography. This theoretical approach to image analysis yields a wealth of information that could be incorporated into the mathematical models, and we conclude by describing how current mathematical models might be enhanced by use of this information, and how these models in turn will help to meet some of the major challenges in cancer detection
Most Likely Separation of Intensity and Warping Effects in Image Registration
This paper introduces a class of mixed-effects models for joint modeling of
spatially correlated intensity variation and warping variation in 2D images.
Spatially correlated intensity variation and warp variation are modeled as
random effects, resulting in a nonlinear mixed-effects model that enables
simultaneous estimation of template and model parameters by optimization of the
likelihood function. We propose an algorithm for fitting the model which
alternates estimation of variance parameters and image registration. This
approach avoids the potential estimation bias in the template estimate that
arises when treating registration as a preprocessing step. We apply the model
to datasets of facial images and 2D brain magnetic resonance images to
illustrate the simultaneous estimation and prediction of intensity and warp
effects
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
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