Multi­Resolution Registration and Segmentation for cardiac BOLD MRI

Ilkay Oksuz1,2 , Rohan Dharmakumar3,4 , and Sotirios A. Tsaftaris2,5

1 Diagnostic Radiology, Yale University, New Haven, CT, United States, 2 IMT Institute for Advanced Studies Lucca, Lucca, Italy, 3 Biomedical Imaging Research Institute, Cedars Sinai Medical Center, Los
Angeles, CA, United States, 4 University of California, Los Angeles, CA, United States, 5 The University of Edinburgh, Edinburgh, United Kingdom

Synopsis

Cardiac Phase­resolved Blood Oxygen­Level­Dependent (CP­BOLD) MRI is a new contrast and stress­free approach for detecting
myocardial ischemia, that identifies the ischemic myocardium by examining changes in myocardial signal intensity patterns as a function
of cardiac phase. But, these changes coupled with cardiac motion, challenge automated standard CINE MR myocardial segmentation and
registration techniques resulting in a significant drop of segmentation and registration accuracy. We propose a dictionary learning based
multi­resolution registration scheme for supervised learning and sparse representation of the myocardium. Our results show an
improvement of 15% myocardial segmentation w.r.t. the state of the art.
Introduction
Cardiac Phase­resolved Blood Oxygen­Level­Dependent (CP­BOLD) MRI1 is a new contrast and stress­free approach for detecting myocardial
ischemia, that identifies the ischemic myocardium by examining changes in myocardial signal intensity as a function of cardiac phase. Visualizing and
detecting these changes requires significant post­processing, including myocardial segmentation for isolating the myocardium and registration to
establish correspondence among the cardiac images in this cine acquisition. Automated analysis approaches which can obtain pixel­level
determination of ischemia are desirable, since they may lead to improved transmural assessment of the extent of ischemia. But, changes in
myocardial intensity patterns and myocardial shape (due to the heart's motion) challenge automated standard CINE MR myocardial segmentation and
registration techniques resulting in a significant drop of segmentation and registration accuracy.
Purpose

We hypothesize that using a multi­resolution dictionary based registration approach and iterative refinement can improve myocardial segmentation
accuracy. In this work, myocardial segmentation accuracy is evaluated on CP­BOLD data at rest under baseline and stenosis conditions.
Methods

Imaging Studies: Flow­ and motion­compensated 2D short­axis CP­BOLD was acquired along the mid­ventricle in 10 canines at baseline and under
severe LAD stenosis. Imaging studies were performed on a 1.5T Espree (Siemens Healthcare). TR/TE 6.2/3.1ms; spatial resolution=1.2x1.2x8 mm3,
flip­angle=70°, ~25 frames per cardiac cycle. Image Processing: The main principle of the approach (Fig. 1) is to use an external initial database of
pre­segmented images (and dictionaries for myocardium and background) to first come up with an initial segmentation (relying on classification when
projecting on discriminatory dictionaries) for an unseen CP­BOLD dataset (cine acquisition).3 Then it registers images in a multi­resolution fashion
across the cardiac cycle using a new registration algorithm4 that relies on the sparse coefficients. This step refines the obtained segmentation, which
is used to update the dictionaries (adapting them to the dataset under consideration), and thus personalize the process. This process is repeated till
convergence. To obtain an initial dictionary on prior available segmented data sets, at the coarsest resolution, first 9x9 patches are extracted for each
pixel and concatenated with HOG and Gabor features for each patch and dictionaries DB and DM are learned. Multi­Resolution Registration
Refinement: As highlighted in Fig. 2, for each pixel p when projected on the background or myocardium dictionaries sparse coefficients XB and
myocardium XM are obtained and concatenated; Xp =[ XB ;XM ]. They are used to define a similarity metric between two images as: $$$ S(I_{t}
(p),I_{t+1}(p+u))= \mid \mid X^{t}_{p}­X^{t+1}_{p+u} \mid \mid_{1} $$$ .4 Starting at the coarsest resolution, after all images in the cardiac cycle have
been registered, individual per­image segmentations of the myocardium are obtained and propagated to the first image. Then labels are fused (via
majority voting) to refine the segmentation of that image. The segmentation is upscaled and using the corresponding intensity image, new dictionaries
D’B and D’M specific to this image resolution are obtained (Fig. 3). The process iterates using these new dictionaries and sparse representations. At
the finest resolution all images It+j, j≠0 are registered to It, segmentations obtained via the dictionaries for It±j are propagated to It and fused with
majority voting to obtain the final segmentation. Statistical analysis: To evaluate segmentation accuracy, delineations (ground truth) provided by
experts are used. For a given unseen dataset, overlap of the segmentation of It with corresponding ground truth is measured using the Dice overlap
metric, and averaged across all t. Multiple paired t­tests were applied to evaluate performance when compared to state­of­the­art registration
methods, namely Diffeomorphic Demons5, Free Form Deformations (FFD)6, DRAMMS7 and MIND8.
Results
Dice accuracies are presented in Table 1, across our study population. Utilizing the proposed scheme increases myocardial segmentation accuracy
under baseline (#, p<0.001) and ischemia ($, p<0.001) significantly. Exemplary results are shown in Fig. 4 highlighting the importance of multi­
resolution and iterative refinement.
Discussion
The scheme herein improves myocardial segmentation accuracy in a statistically significant manner by refining and adapting the dictionary to the data
using multiple resolutions. When only an external dictionary is used the resulting performance is not different to other methods. However, taking
advantage of registration to refine the segmentation results leads to an improvement by 8%. Operating at multiple resolutions (capturing more context
and spatial information and avoiding local minima) leads to even better improvement (15%).
Conclusions
BOLD contrast affects the performance of image analysis algorithms and here a new scheme of iterative segmentation/registration is proposed. While
the results are remarkable, further improvements are necessary to enable pixel­level assessment of ischemia. When combined with developments in
3D BOLD acquisitions a repeatable, truly non­invasive diagnosis of ischemic heart disease can be made possible.9
Acknowledgements
This work is partially supported by US National Institutes of Health, National Heart Lung and Blood Institute, (grant no: 2R01HL091989­05).
References
1. Tsaftaris et al., Ischemic extent as a biomarker for characterizing severity of coronary artery stenosis with blood oxygen­sensitive MRI, JMRI 35(6),
1338­1348, 2012.

2. Tsaftaris et al., Detecting myocardial ischemia at rest with cardiac phase resolved blood oxygen level dependent cardiovascular magnetic
resonance. Circulation: Cardiovascular Imaging, 6(2), 311­319, 2013.

3. Mukhopadhyay et al., Data­Driven Feature Learning for Myocardial Segmentationof CP­BOLD MRI, FIMH, 189­197, 2015.
4. Oksuz et al., Dictionary Learning Based Image Descriptor for Myocardial Registration of CP­BOLD MR, MICCAI 205­213, 2015.

5. Vercauteren et al., Non­parametric diffeomorphic image registration with the demons algorithm, MICCAI, 319­326, 2007.

6. Rueckert et al., Nonrigid registration using free­form deformations: application to breast MR images, TMI 18(8), 712­721, 1999.

7. Ou et al., DRAMMS: Deformable registration via attribute matching and mutual­saliency weighting, MIA 15(4), 622­639, 2011.

8. Heinrich et al., MIND: Modality independent neighbourhood descriptor for multi­modal deformable registration, MIA, 16(7), 1423­1435, 2012.

9. Yang et al., Fast, whole­heart, free­breathing 3D T2 mapping at 3T with application to myocardial edema imaging, JCMR 17(1), Q125, 2015.
Figures

Figure 1: Flowchart of the proposed algorithm. The images at different cardiac phases are down­sampled and registered at different resolutions (Fig. 2). The transformations from the coarser scale are used
as guidance to update the dictionaries for the finer scale registration process in dictionary learning based registration (Fig. 3).

Figure 2: Dictionary learning based registration. At every resolution patches are extracted from fixed and moving images to calculate the sparse representations. Dictionary learning based similarity metric is
used in an optimization framework to find displacements. These displacements are used to update the dictionaries for the next resolution.

Figure 3: Upscaling and dictionary update. At every resolution the calculated displacements are used to generate label fusion from multiple cardiac phases on the fixed image. Then, these label maps are
upscaled and used to obtain new dictionaries specific to this unseen image in the new resolution.
Figure 4: (a) Original. (b) Initial segmentation presents holes and irregularities. However, as soon as images across the cardiac cycle are registered, the segmentation is refined (c). Adding multiple resolutions
and updating the dictionaries accordingly leads to the proposed approach (d) comes close to the ground truth (e).

Table 1: Dice overlap comparison (mean±std) of the myocardial segmentation accuracy

Proc. Intl. Soc. Mag. Reson. Med. 24 (2016) 0415