1,090 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
Spatio-temporal motion correction and iterative reconstruction of in-utero fetal fMRI
Resting-state functional Magnetic Resonance Imaging (fMRI) is a powerful
imaging technique for studying functional development of the brain in utero.
However, unpredictable and excessive movement of fetuses have limited its
clinical applicability. Previous studies have focused primarily on the accurate
estimation of the motion parameters employing a single step 3D interpolation at
each individual time frame to recover a motion-free 4D fMRI image. Using only
information from a 3D spatial neighborhood neglects the temporal structure of
fMRI and useful information from neighboring timepoints. Here, we propose a
novel technique based on four dimensional iterative reconstruction of the
motion scattered fMRI slices. Quantitative evaluation of the proposed method on
a cohort of real clinical fetal fMRI data indicates improvement of
reconstruction quality compared to the conventional 3D interpolation
approaches.Comment: Accepted by MICCAI 202
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
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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
Dynamic Neural Fields for Learning Atlases of 4D Fetal MRI Time-series
We present a method for fast biomedical image atlas construction using neural
fields. Atlases are key to biomedical image analysis tasks, yet conventional
and deep network estimation methods remain time-intensive. In this preliminary
work, we frame subject-specific atlas building as learning a neural field of
deformable spatiotemporal observations. We apply our method to learning
subject-specific atlases and motion stabilization of dynamic BOLD MRI
time-series of fetuses in utero. Our method yields high-quality atlases of
fetal BOLD time-series with 5-7 faster convergence compared to
existing work. While our method slightly underperforms well-tuned baselines in
terms of anatomical overlap, it estimates templates significantly faster, thus
enabling rapid processing and stabilization of large databases of 4D dynamic
MRI acquisitions. Code is available at
https://github.com/Kidrauh/neural-atlasingComment: 6 pages, 2 figures. Accepted by Medical Imaging Meets NeurIPS 202
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
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