586 research outputs found
Temporal Registration in In-Utero Volumetric MRI Time Series
We present a robust method to correct for motion and deformations in in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames. We demonstrate the utility of the temporal model by showing that its use improves the accuracy of the segmentation propagation through temporal registration. Our results suggest that the proposed model captures accurately the temporal dynamics of deformations in in-utero MRI time series.National Institutes of Health (U.S.) (NIH NIBIB NAC P41EB015902)National Institutes of Health (U.S.) (NIH NICHD U01HD087211)National Institutes of Health (U.S.) (NIH NIBIB R01EB017337)Wistron CorporationMerrill Lynch Wealth Management (Fellowship
Temporal Registration in In-Utero Volumetric MRI Time Series
We present a robust method to correct for motion and deformations in in-utero volumetric MRI time series. Spatio-temporal analysis of dynamic MRI requires robust alignment across time in the presence of substantial and unpredictable motion. We make a Markov assumption on the nature of deformations to take advantage of the temporal structure in the image data. Forward message passing in the corresponding hidden Markov model (HMM) yields an estimation algorithm that only has to account for relatively small motion between consecutive frames. We demonstrate the utility of the temporal model by showing that its use improves the accuracy of the segmentation propagation through temporal registration. Our results suggest that the proposed model captures accurately the temporal dynamics of deformations in in-utero MRI time series.National Institutes of Health (U.S.) (NIH NIBIB NAC P41EB015902)National Institutes of Health (U.S.) (NIH NICHD U01HD087211)National Institutes of Health (U.S.) (NIH NIBIB R01EB017337)Wistron CorporationMerrill Lynch Wealth Management (Fellowship
A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth.
Longitudinal characterization of early brain growth in-utero has been limited by a number of challenges in fetal imaging, the rapid change in size, shape and volume of the developing brain, and the consequent lack of suitable algorithms for fetal brain image analysis. There is a need for an improved digital brain atlas of the spatiotemporal maturation of the fetal brain extending over the key developmental periods. We have developed an algorithm for construction of an unbiased four-dimensional atlas of the developing fetal brain by integrating symmetric diffeomorphic deformable registration in space with kernel regression in age. We applied this new algorithm to construct a spatiotemporal atlas from MRI of 81 normal fetuses scanned between 19 and 39 weeks of gestation and labeled the structures of the developing brain. We evaluated the use of this atlas and additional individual fetal brain MRI atlases for completely automatic multi-atlas segmentation of fetal brain MRI. The atlas is available online as a reference for anatomy and for registration and segmentation, to aid in connectivity analysis, and for groupwise and longitudinal analysis of early brain growth
Predicting Slice-to-Volume Transformation in Presence of Arbitrary Subject Motion
This paper aims to solve a fundamental problem in intensity-based 2D/3D
registration, which concerns the limited capture range and need for very good
initialization of state-of-the-art image registration methods. We propose a
regression approach that learns to predict rotation and translations of
arbitrary 2D image slices from 3D volumes, with respect to a learned canonical
atlas co-ordinate system. To this end, we utilize Convolutional Neural Networks
(CNNs) to learn the highly complex regression function that maps 2D image
slices into their correct position and orientation in 3D space. Our approach is
attractive in challenging imaging scenarios, where significant subject motion
complicates reconstruction performance of 3D volumes from 2D slice data. We
extensively evaluate the effectiveness of our approach quantitatively on
simulated MRI brain data with extreme random motion. We further demonstrate
qualitative results on fetal MRI where our method is integrated into a full
reconstruction and motion compensation pipeline. With our CNN regression
approach we obtain an average prediction error of 7mm on simulated data, and
convincing reconstruction quality of images of very young fetuses where
previous methods fail. We further discuss applications to Computed Tomography
and X-ray projections. Our approach is a general solution to the 2D/3D
initialization problem. It is computationally efficient, with prediction times
per slice of a few milliseconds, making it suitable for real-time scenarios.Comment: 8 pages, 4 figures, 6 pages supplemental material, currently under
review for MICCAI 201
Magnetic Resonance Imaging of the Brain in Moving Subjects. Application of Fetal, Neonatal and Adult Brain Studies
Imaging in the presence of subject motion has been an ongoing challenge for
magnetic resonance imaging (MRI). Motion makes MRI data inconsistent, causing
artifacts in conventional anatomical imaging as well as invalidating diffusion
tensor imaging (DTI) reconstruction. In this thesis some of the important issues
regarding the acquisition and reconstruction of anatomical and DTI imaging of
moving subjects are addressed; methods to achieve high resolution and high signalto-
noise ratio (SNR) volume data are proposed.
An approach has been developed that uses multiple overlapped dynamic single shot
slice by slice imaging combined with retrospective alignment and data fusion to
produce self consistent 3D volume images under subject motion. We term this
method as snapshot MRI with volume reconstruction or SVR. The SVR method
has been performed successfully for brain studies on subjects that cannot stay still,
and in some cases were moving substantially during scanning. For example, awake
neonates, deliberately moved adults and, especially, on fetuses, for which no
conventional high resolution 3D method is currently available. Fine structure of the
in-utero fetal brain is clearly revealed for the first time with substantially improved
SNR. The SVR method has been extended to correct motion artifacts from
conventional multi-slice sequences when the subject drifts in position during data
acquisition.
Besides anatomical imaging, the SVR method has also been further extended to
DTI reconstruction when there is subject motion. This has been validated
successfully from an adult who was deliberately moving and then applied to inutero
fetal brain imaging, which no conventional high resolution 3D method is
currently available. Excellent fetal brain 3D apparent diffusion coefficient (ADC)
maps in high resolution have been achieved for the first time as well as promising
fractional Anisotropy (FA) maps.
Pilot clinical studies using SVR reconstructed data to study fetal brain development
in-utero have been performed. Growth curves for the normally developing fetal
brain have been devised by the quantification of cerebral and cerebellar volumes as
well as some one dimensional measurements. A Verhulst model is proposed to
describe these growth curves, and this approach has achieved a correlation over
0.99 between the fitted model and actual data
Fetal whole-heart 4D imaging using motion-corrected multi-planar real-time MRI
Purpose: To develop a MRI acquisition and reconstruction framework for
volumetric cine visualisation of the fetal heart and great vessels in the
presence of maternal and fetal motion.
Methods: Four-dimensional depiction was achieved using a highly-accelerated
multi-planar real-time balanced steady state free precession acquisition
combined with retrospective image-domain techniques for motion correction,
cardiac synchronisation and outlier rejection. The framework was evaluated and
optimised using a numerical phantom, and evaluated in a study of 20 mid- to
late-gestational age human fetal subjects. Reconstructed cine volumes were
evaluated by experienced cardiologists and compared with matched ultrasound. A
preliminary assessment of flow-sensitive reconstruction using the velocity
information encoded in the phase of dynamic images is included.
Results: Reconstructed cine volumes could be visualised in any 2D plane
without the need for highly-specific scan plane prescription prior to
acquisition or for maternal breath hold to minimise motion. Reconstruction was
fully automated aside from user-specified masks of the fetal heart and chest.
The framework proved robust when applied to fetal data and simulations
confirmed that spatial and temporal features could be reliably recovered.
Expert evaluation suggested the reconstructed volumes can be used for
comprehensive assessment of the fetal heart, either as an adjunct to ultrasound
or in combination with other MRI techniques.
Conclusion: The proposed methods show promise as a framework for
motion-compensated 4D assessment of the fetal heart and great vessels
AFFIRM: Affinity Fusion-based Framework for Iteratively Random Motion correction of multi-slice fetal brain MRI
Multi-slice magnetic resonance images of the fetal brain are usually
contaminated by severe and arbitrary fetal and maternal motion. Hence, stable
and robust motion correction is necessary to reconstruct high-resolution 3D
fetal brain volume for clinical diagnosis and quantitative analysis. However,
the conventional registration-based correction has a limited capture range and
is insufficient for detecting relatively large motions. Here, we present a
novel Affinity Fusion-based Framework for Iteratively Random Motion (AFFIRM)
correction of the multi-slice fetal brain MRI. It learns the sequential motion
from multiple stacks of slices and integrates the features between 2D slices
and reconstructed 3D volume using affinity fusion, which resembles the
iterations between slice-to-volume registration and volumetric reconstruction
in the regular pipeline. The method accurately estimates the motion regardless
of brain orientations and outperforms other state-of-the-art learning-based
methods on the simulated motion-corrupted data, with a 48.4% reduction of mean
absolute error for rotation and 61.3% for displacement. We then incorporated
AFFIRM into the multi-resolution slice-to-volume registration and tested it on
the real-world fetal MRI scans at different gestation stages. The results
indicated that adding AFFIRM to the conventional pipeline improved the success
rate of fetal brain super-resolution reconstruction from 77.2% to 91.9%
Spatiotemporal alignment of in utero BOLD-MRI series
Purpose: To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs.
Materials and Methods: The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison.
Results: The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P < 0.01) and volume overlap and distance between region boundaries measures were significantly improved (P < 0.01).
Conclusion: The proposed approach to align MRI time series enables more accurate quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs.National Institutes of Health (NIH) . Grant Numbers: U01 HD087211 , R01 EB017337 Consejeria de Educacion, Juventud y Deporte de la Comunidad de Madrid (Spain) through the Madrid-MIT M+Vision Consortium
Normative spatiotemporal fetal brain maturation with satisfactory development at 2 years
Maturation of the human fetal brain should follow precisely scheduled structural growth and folding of the cerebral cortex for optimal postnatal function1 . We present a normative digital atlas of fetal brain maturation based on a prospective international cohort of healthy pregnant women2 , selected using World Health Organization recommendations for growth standards3 . Their fetuses were accurately dated in the first trimester, with satisfactory growth and neurodevelopment from early pregnancy to 2 years of age4,5 . The atlas was produced using 1,059 optimal quality, three dimensional ultrasound brain volumes from 899 of the fetuses and an automated analysis pipeline6–8 . The atlas corresponds structurally to published magnetic resonance images9 , but with finer anatomical details in deep grey matter. The between study site variability represented less than 8.0% of the total variance of all brain measures, supporting pooling data from the eight study sites to produce patterns of normative maturation. We have thereby generated an average representation of each cerebral hemisphere between 14 and 31 weeks’ gestation with quantification of intracranial volume variability and growth patterns. Emergent asymmetries were detectable from as early as 14 weeks, with peak asymmetries in regions associated with language development and functional lateralization between 20 and 26 weeks’ gestation. These patterns were validated in 1,487 three-dimensional brain volumes from 1,295 different fetuses in the same cohort. We provide a unique spatiotemporal benchmark of fetal brain maturation from a large cohort with normative postnatal growth and neurodevelopment
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