8,801 research outputs found
PyMorph: Automated Galaxy Structural Parameter Estimation using Python
We present a new software pipeline -- PyMorph -- for automated estimation of
structural parameters of galaxies. Both parametric fits through a two
dimensional bulge disk decomposition as well as structural parameter
measurements like concentration, asymmetry etc. are supported. The pipeline is
designed to be easy to use yet flexible; individual software modules can be
replaced with ease. A find-and-fit mode is available so that all galaxies in a
image can be measured with a simple command. A parallel version of the Pymorph
pipeline runs on computer clusters and a Virtual Observatory compatible web
enabled interface is under development.Comment: 15 pages, 12 figures, 1 table, accepted for publication in MNRA
Serial Correlations in Single-Subject fMRI with Sub-Second TR
When performing statistical analysis of single-subject fMRI data, serial
correlations need to be taken into account to allow for valid inference.
Otherwise, the variability in the parameter estimates might be under-estimated
resulting in increased false-positive rates. Serial correlations in fMRI data
are commonly characterized in terms of a first-order autoregressive (AR)
process and then removed via pre-whitening. The required noise model for the
pre-whitening depends on a number of parameters, particularly the repetition
time (TR). Here we investigate how the sub-second temporal resolution provided
by simultaneous multislice (SMS) imaging changes the noise structure in fMRI
time series. We fit a higher-order AR model and then estimate the optimal AR
model order for a sequence with a TR of less than 600 ms providing whole brain
coverage. We show that physiological noise modelling successfully reduces the
required AR model order, but remaining serial correlations necessitate an
advanced noise model. We conclude that commonly used noise models, such as the
AR(1) model, are inadequate for modelling serial correlations in fMRI using
sub-second TRs. Rather, physiological noise modelling in combination with
advanced pre-whitening schemes enable valid inference in single-subject
analysis using fast fMRI sequences
Hybrid Active Contour Based on Local and Global Statistics Parameterized by Weight Coefficients for Inhomogeneous Image Segmentation
Image inhomogeneity often occurs in real-world images and may present considerable difficulties during image segmentation. Therefore, this paper presents a new approach for the segmentation of inhomogeneous images. The proposed hybrid active contour model is formulated by combining the statistical information of both the local and global region-based energy fitting models. The inclusion of the local region-based energy fitting model assists in extracting the inhomogeneous intensity regions, whereas the curve evolution over the homogeneous regions is accelerated by including the global region-based model in the proposed method. Both the local and global region-based energy functions in the proposed model drag contours toward the accurate object boundaries with precision. Each of the local and global region-based parts are parameterized with weight coefficients, based on image complexity, to modulate two parts. The proposed hybrid model is strongly capable of detecting region of interests (ROIs) in the presence of complex object boundaries and noise, as its local region-based part comprises bias field. Moreover, the proposed method includes a new bias field (NBF) initialization and eliminates the dependence over the initial contour position. Experimental results on synthetic and real-world images, produced by the proposed model, and comparative analysis with previous state-of-the-art methods confirm its superior performance in terms of both time efficiency and segmentation accuracy
Cerebral atrophy in mild cognitive impairment and Alzheimer disease: rates and acceleration.
OBJECTIVE: To quantify the regional and global cerebral atrophy rates and assess acceleration rates in healthy controls, subjects with mild cognitive impairment (MCI), and subjects with mild Alzheimer disease (AD). METHODS: Using 0-, 6-, 12-, 18-, 24-, and 36-month MRI scans of controls and subjects with MCI and AD from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we calculated volume change of whole brain, hippocampus, and ventricles between all pairs of scans using the boundary shift integral. RESULTS: We found no evidence of acceleration in whole-brain atrophy rates in any group. There was evidence that hippocampal atrophy rates in MCI subjects accelerate by 0.22%/year2 on average (p = 0.037). There was evidence of acceleration in rates of ventricular enlargement in subjects with MCI (p = 0.001) and AD (p < 0.001), with rates estimated to increase by 0.27 mL/year2 (95% confidence interval 0.12, 0.43) and 0.88 mL/year2 (95% confidence interval 0.47, 1.29), respectively. A post hoc analysis suggested that the acceleration of hippocampal loss in MCI subjects was mainly driven by the MCI subjects that were observed to progress to clinical AD within 3 years of baseline, with this group showing hippocampal atrophy rate acceleration of 0.50%/year2 (p = 0.003). CONCLUSIONS: The small acceleration rates suggest a long period of transition to the pathologic losses seen in clinical AD. The acceleration in hippocampal atrophy rates in MCI subjects in the ADNI seems to be driven by those MCI subjects who concurrently progressed to a clinical diagnosis of AD
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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