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A survey of shaped-based registration and segmentation techniques

for cardiac images


Vahid Tavakoli

, Amir A. Amini
1
University of Louisville, Louisville, KY, United States
a r t i c l e i n f o
Article history:
Available online 30 April 2013
Keywords:
Cardiac CT
Cardiac motion
Cardiac MR
Cardiac segmentation
Cardiac registration
Echocardiography
Review article
a b s t r a c t
Heart disease is the leading cause of death in the modern world. Cardiac imaging is routinely applied for
assessment and diagnosis of cardiac diseases. Computerized image analysis methods are now widely
applied to cardiac segmentation and registration in order to extract the anatomy and contractile function
of the heart. The vast number of recent papers on this topic point to the need for an up to date survey in
order to summarize and classify the published literature. This paper presents a survey of shape modeling
applications to cardiac image analysis from MRI, CT, echocardiography, PET, and SPECT and aims to (1)
introduce new methodologies in this eld, (2) classify major contributions in image-based cardiac mod-
eling, (3) provide a tutorial to beginners to initiate their own studies, and (4) introduce the major chal-
lenges of registration and segmentation and provide practical examples. The techniques surveyed include
statistical models, deformable models/level sets, biophysical models, and non-rigid registration using
basis functions. About 130 journal articles are categorized based on methodology, output, imaging sys-
tem, modality, and validations. The advantages and disadvantages of the registration and validation tech-
niques are discussed as appropriate in each section.
2013 Elsevier Inc. All rights reserved.
1. Introduction
The heart is the most energetic organ in our body. Beating about
every second, it continuously supplies the body with vital oxygen-
carrying blood. Heart disease is the leading cause of death in
modern countries [13]. The mortality rate of CVD is estimated
to be 17 million in 2005 and thus is ranked as the top killer world-
wide [35]. According to the AHA update of 2009, CVD is the cause
of 10% of days of lost productivity in low- and middle-income
countries, and 18% of days of lost productivity in high income
countries. CVD morbidity rates are estimated to rise from around
47 million days globally in 1990 to 82 million days in 2020 [46].
Analysis of the cardiac function using imaging instruments has
shown to be effective in reducing the mortality and morbidity of
CVD. Myocardial motion analysis is time consuming and suffers
from inter and intra-observer variability. Computerized analysis
can help clinicians to interpret the medical conditions objectively
[1,79]. Cardiac image processing techniques, mainly categorized
as segmentation and registration, have been used widely to assess
the functionality of the heart [1014]. Cardiac image segmentation
provides us with high quality structural information of the heart
while registration techniques calculate the local functional analy-
sis helpful in diagnosis and treatment planning of patients. Model-
ing of the cardiac shape, motion and physical structure have played
a major role in the development of the image analysis algorithms.
Previously, there have been some review papers in the eld of
computer analysis of cardiac imaging [15,16]. Some review papers
have focused on echocardiography segmentation [17], cine MR
segmentation [18] or Tagged MRI [19,20]. Frangi et al. [16] classi-
ed cardiac modeling techniques to three classes: surface models,
1077-3142/$ - see front matter 2013 Elsevier Inc. All rights reserved.
http://dx.doi.org/10.1016/j.cviu.2012.11.017
Abbreviations: AAM, Active Appearance Model; ASM, Active Shape Model; CT,
Computed Tomography; CVD, Cardiovascular Disease; MRI, Magnetic Resonance
Imaging; EB, Expert Based; EDV, End Diastolic Volume; EF, Ejection Fraction; EFFD,
Extended Free Form Deformation; EM, Expectation Maximization; Endo, Endocar-
dium; Epi, Epicardium; ESV, End Systolic Volume; FE, Finite Element; FFD, Free
Form Deformation; GMM, Gaussian Mixture Model; Four CH, Four chamber; GRPM,
Generalized Robust Point Matching; LA, Left Atrium; LADA, Left Anterior Descend-
ing Artery; LAX, Long Axis; LCX, Left Circumex; LV, Left Ventricle; MI, Mutual
Information; MIA, Medical Image Analysis; MRI, Magnetic Resonance Imaging; MRF,
Markov Random Field; N, Normal; NMI, Normalized Mutual Information; N/A, Not
Applicable; NURBS, Non-Uniform Rational B-Spline; P, Patient; PCA, Principal
Component Analysis; PET, Positron Emission Tomography; PM, Papillary Muscle;
RA, Right Atrium; RPM, Robust Point Matching; RV, Right Ventricle; SAD, Sum
Absolute of Differences; SAX, Short Axis; SM, Sonomicrometry; SPECT, Single
Photon Emission Computed Tomography; SSD, Sum Square of Differences; TDI,
Tissue Doppler Imaging; TEE, Trans-Esophageal Echocardiography; TMI, Transac-
tion of Medical Imaging; US, Ultrasound.

Corresponding author. Address: Room 410, Lutz Hall, University of Louisville,


Louisville, KY 40292, United States. Fax: +1 502 8764534.
E-mail addresses: v0tava01@louisville.edu (V. Tavakoli), amir.amini@louisville.
edu (A.A. Amini).
1
Address: Room 409, Lutz Hall, University of Louisville, Louisville, KY 40292,
United States. Fax: +1 502 8764534.
Computer Vision and Image Understanding 117 (2013) 966989
Contents lists available at SciVerse ScienceDirect
Computer Vision and Image Understanding
j our nal homepage: www. el sevi er. com/ l ocat e/ cvi u
volume models, and deformable models. The review focused on 3D
cardiac modeling techniques based on different modalities namely
angiography, cardiac US, isotope imaging, cardiac CT, and MRI.
With the increasing number of the cardiac modeling techniques,
a review article to summarize recent efforts is timely.
This survey aims to (1) classify major contributions in the eld
of cardiac modeling, (2) introduce the methodologies in this eld,
(3) tutor beginners to initiate their research, and (4) introduce
the major challenges of registration and segmentation with exam-
ples. The techniques developed in the last 10 years are classied
as: statistical models, deformable models/level sets, biophysical
models, and non-rigid registration methods. The articles are classi-
ed in different tables describing the method, database, and output
of the technique. The novelties of the methods are described in rel-
evant sections and are compared to alternative algorithms. The
advantages and disadvantages of each category are discussed as
well and different approaches to validation are classied.
The surveyed articles in this review are from major journals
such as IEEE Transaction on Medical Imaging, Medical Image Anal-
ysis, IEEE Transaction on Image Processing, IEEE Transaction on
Information on Biomedicine, Ultrasound in Medicine and Biology,
International Journal of Computer Vision, Computer Vision and Im-
age Understanding, IEEE Transaction on Biomedical Engineering,
Cardiovascular Magnetic Resonance, and Journal of Magnetic Reso-
nance in Medicine.
1.1. Cardiac anatomy
The heart is composed of a muscular contractile organ (myocar-
dium) surrounded by two layers of connective tissue inside and
outside called endocardium and epicardium, respectively. The
heart has four chambers and four major valves (Fig. 1). LV, the
prominent chamber of the heart, is the major contractile chamber,
and maintains the systemic circulation. Myocardial contraction is
maintained by a circulatory system of coronary arteries that sup-
plies the muscle with oxygenized hemoglobin and nutrients. Coro-
nary arteries (right and left) are two branches of the aorta and
supply the myocardium through smaller branches such as LCX,
LAD and diagonal arteries [2].
Due to atherosclerosis, the coronary arteries may gradually be-
come occluded and end in CAD (Coronary Artery Disease).
Coronary occlusion leads to disturbance in the cardiac contractility
and causes global or regional dysfunction in the heart and may be
diagnosed using state-of-the-art medical imaging techniques such
as echocardiography, MRI, CT, and nuclear medicine [2]. In study-
ing ventricular motion, physicians typically assign a subjective seg-
mental function score to different segments of the ventricles:
Normokinesia (0): The myocardial motion and thickening is
normal.
Hypokinesisa (1): The affected segment moves slower and
thickens less than normal.
Akinesia (2): The infarcted region has totally lost its ability to
contract in the systolic phase and moves passively along with
its surrounding myocardial tissue.
Dyskinesisa (3): The infarcted region moves paradoxically and
bulges out during systole due to the ventricular blood pressure.
Aneurysm (4): The infarcted region undergoes remodeling,
becomes thin, bulging outwards during the systolic phase like
a balloon, leading to rupture and death [9].
The cardiac blood circulation is an alternation of two phases:
diastole (relaxation phase) and systole (contraction phase). Nor-
mally 70% of the whole LV blood in end diastole is ejected out dur-
ing systole. The Ejection Fraction (EF) ratio is an index of global LV
function. EF is calculated as (EDVESV)/EDV where EDV is the vol-
ume of the LV at end-diastole and ESV is the volume of the LV dur-
ing end-systole. Ventricular walls thicken during systole this is
typically referred to as wall thickening and has been proven to
be a very reliable index of regional myocardial function. Heart fail-
ure is characterized by a signicant decrease in the EF. An addi-
tional index of cardiac performance is myocardial mass which
can be determined frommyocardial volume, assuming the myocar-
dium to have uniform density [9].
2. Cardiac imaging modalities
There are several cardiac imaging modalities that are in wide-
spread use. These include MRI, CT, echocardiography, and nuclear
medicine. Each method has advantages and draw backs that are dis-
cussedinthis section. MRI, CT, andEchocardiographyare amenableto
computer analysis and much effort has been devoted to automated
processing of images from these modalities. In comparison, nuclear
medicine has seen less effort devoted to computerized analysis.
2.1. MRI
Magnetic Resonance Imaging (MRI) uses a magnetic eld to
align the magnetization of hydrogen nuclei in the body. Subse-
quently radio frequency pulses change the alignment of this mag-
netization and produce a rotating magnetic eld detectable by an
external RF coil. MRI uses non-ionizing radiation and is considered
a non-invasive technique. Contrast may be used for further signal
enhancement. Contraindications to use of MRI include pacemakers
and metal implants. With MRI, different segments of the myocar-
dium are well visualized and can be easily reconstructed in 4D for-
mat. An advantage of MRI is that it is possible to acquire images
with different orientation with no image processing (no reslicing
is necessary). An advantage of MRI in comparison to other imaging
methods is that it permits evaluation of perfusion (rst past perfu-
sion), function (cine and tagged imaging), scars (Late-Gadolinium
Enhancement imaging), as well as epicardial coronaries. However,
MRI is more costly than other methods, (particularly echocardiog-
raphy) and is not available in all cardiac care centers. Cine MR is
able to achieve high resolution images with respect to the cardiac
border but the contrast is not as helpful inside the cardiac wall.
Fig. 1. Anatomical components of the heart labeled separately as LV, RV, LA, RA,
Aortic valve (A), Tricuspid valve (T), Pulmonic valve (P), Mitral valve (M). (From Yale
cardiac atlas: www.yale.edu/imaging/contents.html.)
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 967
An MR imaging protocol named tagged MRI uses spin tagging pre-
pulses to produce markers inside the myocardiumover time, which
can be tracked, permitting the possibility to compute dense myo-
cardial motions and the strain. One drawback of this method is
the fading of the tag lines over time, which is especially pronounced
in diastole, when imaging with no trigger delay. A solution to this is
to apply a trigger delay in order to visualize diastolic function of the
heart. Cardiac cine-MRI is considered the standard MR technique
mainly used for global function measurements and segmentation
while tagged MR techniques are used for regional analysis and tem-
poral registration [7]. MR images acquired with orientation perpen-
dicular to the long axis of the heart (the line which connects the
apex to the outow tract) is called Short Axis plane (SAX) (Fig. 2).
Imaging of the heart in cine MRI covers about 1015 slices and
1530 frames, depending on the size of the heart, prescribed slice
thickness, the heart rate, and specic approach to image acquisi-
tion. Fig. 3 shows SAX images in cine and tagged MR series during
different cardiac cycles. Images acquired parallel to the long-axis
axis are called Long Axis (LAX) images and are sometimes combined
with SAX images for better visualization of the anatomy as well as
for computing true 3-D motion (including the through-plane mo-
tion). Cardiac images are not specic to the heart and certainly in-
clude non-cardiac tissue as well. To decrease the computational
time, a region of interest (ROI) can be computed that only includes
the heart tissue. On a usual (gradient echo) cine MR image, the
blood pools is white and the myocardium is black; however, black
blood imaging renders the blood pool dark [7,19,20]. Other submo-
dalities of CMR include Late-Gadolinium-Enhancement (LGE) imag-
ing for visualizing scarred tissue, coronary MRA for visualizing the
coronaries, multinuclear spectroscopy for spectroscopic imaging
based on Carbon, Sodium, or Flourine, and rst-pass perfusion
imaging to visualize the ischemic myocardium. Flow imaging
(e.g., phase-contrast) MRI can also be used to reveal ow and mo-
tion information for blood owinside vessels which may be located
deep within the body or to determine ventricular wall motion [7].
2.2. Echocardiography
Echocardiography utilizes the backscattered ultrasound wave
generated by an array of piezoelectric crystals to acquire images of
different tissues. It has important advantages including, portability,
non-invasiveness, use of non-ionizing radiation, real-time, and low
cost. However, echocardiography, in general, suffers frompoor con-
trast, noisy images, sub-optimal visualization of the cardiac seg-
ments, air/bone interaction problems causing reverberation
artifacts, and reproducibility and operator dependence issues. An
additional disadvantage in the overweight patients is the inability
to obtain an acoustic window since there is a need to bypass the
lungs and the ribcage to image the heart [8,9]. Doppler imaging is
possible withUS andmay be usedto compute the velocity of moving
particles (andmeasure bloodow). However, use of Doppler US only
permits computation of the tissue/blood motion in the direction of
the ultrasound beam (called the angle of insonication) [8,9].
3D echocardiography images can be obtained using recent
sophisticated 3D ultrasound transducers by using a miniaturized
array of piezoelectric crystals. Real time 3D scanners were intro-
duced in the early 1990s but in comparison to 2D echocardiogra-
phy, initial images suffered from low spatial resolution. New
high-tech transducer arrays have signicantly improved spatial
resolution and image quality as a result, 3D imaging is enjoying
more wide-spread use [8,9].
Fig. 2. (a) Illustration of Short-Axis (SAX) and Long-Axis (LAX) cardiac images in a normal subject, (b) cardiac Cine MRI, LAX (C) Cardiac Cine MRI SAX (1:LV, 2:RV), (d) A close-
up of the SAX image showing the epicardium and endocardium and Papillary Muscles (PMs) shape variability.
968 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
Ultrasound images have a texture pattern usually referred to as
speckle. Speckle formation is the result of the diffuse scattering of
the ultrasound wave encountering random interference with scat-
terers which are very tiny particles of size comparable to the wave-
length of the ultrasound wave. These scatterer particles do not
simply reect or refract the ultrasound wave but induce a more
complex diffuse scattering which is the basic physical concept of
speckle formation. Speckle is considered an inherent property of
the ultrasound image notorious for having spatial correlated mul-
tiplicative noise and making the ultrasound images unreliable.
Speckle tracking techniques try to use these same speckle patterns
to detect the cardiac motion in echocardiographic frames. Doppler
imaging is also utilized for computing the velocity of blood as well
as that of the myocardium. When applied to image tissue veloci-
ties, the technique is referred to as Tissue Doppler Imaging or
TDI for short [8,9].
2.3. CT
4D cardiac CT allows non-invasive imaging of the detailed car-
diac anatomy with high contrast and exquisite resolution; espe-
cially useful for the assessment of coronary artery structure.
However, it is not as widely available as echocardiography and uses
ionizing radiation. Cardiac multi-detector computed tomography
(MDCT) is able to acquire moving images of the heart that rivals
cine MRI (though with reduced temporal resolution) as a detailed
source of information (Fig. 5). Initial generations of CT systems were
not able to provide accurate images of the heart due to its fast mo-
tion. Now a days, MDCT scanners such as 64 (128, 256, or 320)
detector-row CT scanners and dual source CT scanner are available
with multiple gantry rotations in one second acquiring several CT
slices (64 slice for a 64 row CT scanner). It is foreseeable that CT
technology will advance to the point of covering the entire heart
in a single rotation and in a single cardiac cycle. Also, use of iterative
reconstruction techniques has the potential to permit the use of low
dose, high quality scans. CT angiography (CTA) is very sensitive for
diagnosis of coronary artery, by-pass graft, and stent abnormalities.
It is able to acquire unique visualization of the coronary arteries
including narrowing, type and degree of atherosclerosis plaque.
Additionally, it can also be used to simultaneously visualize the pul-
monary and systemic arteries as well as the thrombosis. Despite the
expense, cardiac CT is becoming more widely available in cardiac
care centers and may be an alternative to diagnostic catheterization
which is invasive and costly. Recent advances in cardiac CT with
contrast (late enhancement CT) also permit visualization of scarred
myocardium (similar to LGE imaging in MRI) and also the possibil-
ity to utilize a range of X-ray energies to perform tissue character-
ization (this is referred to spectral CT) [7,8,10].
2.4. Radioisotope imaging
Nuclear medicine techniques such as Positron Emission Tomog-
raphy (PET) and Single Photon Emission Computer Tomography
(SPECT) use the gamma-ray or positron emission of injected radio-
pharmaceuticals in order to image the myocardium. The injected
radiotracers are taken up in particular tissues, such as malfunction-
ing or dead myocardium, and continue to irradiate positrons
(which lead to emission of gamma-rays) during decay, permitting
visualization of the metabolism and function of the heart. SPECT
studies, which make use of Thalium or Technetium, are routinely
utilized to image myocardial perfusion. Imaging can be performed
at rest or under pharmacologic stress (e.g. adenosine) to measure
the perfusion reserve and defects (Fig. 5). The wash-out of the iso-
tope is the long acquisition time which is in the range of 30 min to
3 h while the patient should stay still. Although radio-tracer stud-
ies pose some risk to the patient, they have proven to be extremely
powerful with high sensitivity and specicity in the assessment of
patients with coronary artery disease and in determining the terri-
tory with perfusion defects. Fluroro-Deoxy-Glucose (FDG) is used
in the case of PET to image myocardial metabolism. In fact, with
FDG PET it is possible to distinguish between necrotic vs. stunned
vs. hibernating myocardium. PET is the only modality which can
conclusively determine myocardial viability and is typically used
as ground-truth in multimodality studies [1014].
Albeit the importance and prevalence of nuclear cardiology in
clinical care of patients, nuclear techniques (especially PET) are
very expensive and furthermore the resolutions are nowhere near
other modalities. Perhaps, this has contributed to decreased enthu-
siasm of computer vision researcher to develop automatic and
quantitative techniques for this modality.
2.5. Cardiac segmentation and registration challenges
Cardiac segmentation consists of the segmentation of the epi-
cardium and the endocardium of LV, RV, LA, and RA. Epicardial seg-
mentation: In general epicardial delineation is more difcult than
endocardial delineation due to the similarity and fuzziness of the
gray level of the outer tissues and the heart and poor contrast.
Endocardial contour has a good contrast due to the large intensity
variation of the blood and the myocardium in all the modalities.
Endocardial segmentation: Endocardial delineation is not straight-
forward due to the Papillary Muscles and myocardial trabeculation
ridges visible in MR, echo and CT (Figs. 35). Local image features
such as intensity and gradient do not represent the real contours
near the Papillary Muscle. Since clinicians consider the Papillary
Muscle as a part of the blood pool, it is usually not segmented in
the current algorithms. Some of the challenges are shown in Fig. 6.
Fig. 3. (a) Cine MRI and (b) Tagged MRI data at the basal, mid-LV, and apical sections in different phases of the cardiac cycle in a canines heart (systole to diastole), (1:LV,
2:RV). For the Mid-LV slices good visualization of LV and RV can be achieved due to the larger size of the chamber for these cross section. The apical slices however result in
poor visualizations since these chambers are small or non-existent at the apex. Basal slices on the other hand are complicated with atria and the great vessels.
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 969
2.5.1. RV, RA, LA, and great vessel segmentation
The shape of the RV is also more variable and concave and thus
more challenging than the LV. The RV chamber is present in few
slices and the RV wall is thinner with respect to the LV wall and
therefore the epicardium and endocardium are close to each other
and more difcult to segment. Atria and great vessels are only
present in 24 slices. They are especially difcult to delineate in
echocardiography images but easier to deal with in CT series due
to the better spatial resolution and visibility.
2.5.2. Apical and basal slices
Additionally apical slices are more difcult to segment in all the
modalities due to less information, unpredictable end of the LV and
RV cavities, vicinity of diaphragm, more variable shape and motion
of the contours and haziness of the tissue. Indeed, even manual
segmentation of the tip of the heart (apical slices) is difcult. Basal
slices are also more cumbersome to segment due to highly variable
shape and motion of the LV and RV walls and cavities in the basal
slices as well as the vicinity of the atrial and great vessel lumens.
2.5.3. Pixel resolution anisotropy
Pixel resolution anisotropy is a common issue in MRI and CT
segmentation and registration. The resolution of the pixels in the
spatial direction is not the same as the resolution of the pixel in
the through plane direction.
2.5.4. Motion estimation
With respect to motion estimation, out-of-plane error (through-
plane error) is a common issue in any 2D technique and therefore
3D motion detection is suggested to cope with the problem. How-
ever 3D cardiac imaging usually requires a longer acquisition per-
iod, slice misregistrations, ECG gates, and breath-holding [7].
Fig. 4. Different echocardiographic views with corresponding anatomy (a) transthoracic short-axis view (b) four chamber apical view (From atlas of Echocardiography, http://
www.yale.edu/imaging/echo_atlas/contents/index.htm), (c) a four chamber image, - red boxes show the invisible and dropout regions causing registration and segmentation
challenges. The Papillary Muscles and valve cords can interact with the real endocardial contours as well (1:LV, 2:RV, 3:LA, 4:RA). (For interpretation of the references to color
in this gure legend, the reader is referred to the web version of this article.)
Fig. 5. (a) Cardiac CT SAX image during diastole, (b) cardiac CT SAX image during systole, (c) cardiac SPECT data http://bocaradiology.com/Procedures/cardiac.htm.
Fig. 6. Illustration of some segmentation challenges in cine MR cardiac images: (a) interaction of the neighboring structures in segmentation of epicardium in apical views of
canine cine MRI this is because the LV shape is small and fuzzy, (b) interaction of the neighboring structures in segmentation of LV in basal views of canine cine MRI this is
because the other chambers are comparable in size to the LV for basal locations, (c) interaction of the Papillary Muscle intensity causing the Papillary Muscles to be included
as part of the myocardium in human cine MRI.
970 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
Although cine MRI has excellent cardiac contour contrast, it
lacks the myocardial contrast inside the cardiac wall and, there-
fore, it is not suitable for dense motion analysis and strain estima-
tion. Tagged MRI is suitable for this purpose. The tag line markers
can be tracked through the cardiac frames but they fade out
through the cardiac cycles and are washed out and less useful
especially during the diastole.
2.5.5. Special issues in echocardiography images
Since echocardiography is performed by hand, several views
can be acquired using different transducer orientations. These
views are not the same especially in the task of segmentation. An-
other shortcoming is the fact that in both 2D and 3D echocardiog-
raphy data, the contour of the epicardium or endocardium may be
incomplete simply because it is out of the region of the transducer
coverage. The endocardial and epicardial contours have even less
contrast in echocardiography due to the noisy structure of the
ultrasound images. Different types of ultrasound artifacts contrib-
ute to this problem as well, especially drop out artifact that hap-
pens when the tissue contour is in the direction of the ultrasound
beam. Another feature of ultrasound images is the speckle pattern.
The shift varying PSF in echocardiography makes decorrelation in
the RF signal and the B-mode image which leads to higher error
in the registration methods. Artifacts and the presence of air and
bone also contribute to less accurate results.
3. Methodological classication
Calculation of important cardiac indices such as cardiac vol-
umes and Ejection Fraction are based on accurate segmentation
of the heart chambers while computation of the regional displace-
ments and mechanical indices of cardiac function are related to
temporal registration of the imaging data. Segmentation and regis-
tration can be performed via techniques that will be discussed in
this section.
Bottom up methods: Such as thresholding, morphological, pixel
classication and edge-based techniques were among the rst
techniques to be used in the eld of cardiac image analysis due
to their simple and intuitive nature. However cardiac texture has
a wide intensity range that is not completely detectable by pixel-
driven techniques. Additionally, object boundaries do not neces-
sarily overlay on the edges. This problem can be tackled by using
additional assumptions derived from the cardiac structure, statis-
tics and physics.
A large number of methods have been developed for cardiac
functional and anatomical modeling. In this section, we classify
the modeling techniques into four categories described in Tables
14. These are (1) statistical models, (2) deformable models/level
set, (3) biophysical models, and (4) non-rigid registration using ba-
sis functions. However the boundaries of each class are not exact.
Several papers have combined two or more different classes in
the same algorithm. In this situation, the papers are classied
according to the most relevant group. The tables cover about 130
journal article published in the last 10 years.
Key to the tables: Each table consists of several columns repre-
senting authors, modality, dimension of the method, vendor, out-
put of the algorithm, description of the algorithm, types of
validation, and type of data. The number of cases in the validation
dataset is mentioned in parenthesis as normals (N) or patients (P).
Most of the papers use 2D or 3D human data for validation but
some papers focus on dogs, or computational/ physical phantom
data. The output of the proposed methods can be the contour of
the endocardium only (endo), epicardium (+Epi), RV (+RV), atria
(+A), great vessels (+V), Tag lines (+tag) or motion vectors (+M).
Since any segmentation method delineating the epicardium or
the RV also delineates the endocardium, the key (endo) is used
for methods that only segment the endocardium. In some cases,
parameters such as the number of the data and vendor are missing,
are incomplete or unclear and are left blank in the table.
3.1. Statistical methods
Since intensity is not a perfect descriptor of the contours in car-
diac images, statistical techniques are nding ever increasing
interest in their area. In general, the heart is a convex, and exclud-
ing a few conditions such as a cardiac aneurysm, can be modeled as
an ellipsoidal object that moves in- and out-wards [13]. Therefore
use of statistical priors, including shape, motion or texture, can aid
in the cardiac segmentation and registration tasks. Statistical
methods can be classied based on use of shape prior, Active Shape
Model, Active Appearance Model [21,22] and motion model. Each
subcategory will be discussed separately in this survey. Table 1
contains the statistical articles [2334,22,3570] classied based
on the structure, method, vendor, dataset, and output.
3.1.1. Shape prior
The LV cavity looks like a truncated ellipsoid while the RV cavity
is thinner and crescent shape. The LV wall is three times thicker
than the RV wall. Several authors have tried to use the expected
shape of the heart as a prior in aiding automated segmentation
and registration. The prior is typically incorporated as an addi-
tional constraint to overcome the failures of intensity or edge
based energy functions to uniquely determine the anatomical
boundaries.
3.1.1.1. Simple shapes as prior. Since the LV contour resembles an
ellipse; a fast approach for building a prior is to use an ellipsoid.
Pluempitiwiriyawej et al. [53] utilized an ellipsoid with 5 de-
grees of freedom as prior. The ve parameters dened the loca-
tion, size and scale of the ellipsoid. The distance of the contour
to the ellipsoid was used as the ellipsoid constraint. The authors
also added two additional energy terms for the ellipsoid shape
prior: 1. stochastic region based term based on modeling the dis-
tribution of the pixels inside and outside the contour; 2. an edge
based term similar to a snake (latter will be discussed in Sec-
tion 3.2) energy function to attract the contour toward the
edges. The combined energy functional is used in a level set
framework (latter to be discussed in Section 3.2) in order to seg-
ment 2D short-axis cine MR images. The advantage of this meth-
od is using ve degrees of freedom, which can decrease the
computation.
3.1.1.2. Previous contour. Practically, the shape of contours does not
change dramatically, as they move from one cardiac image to the
next in the spatial or temporal direction. Therefore, a simple ap-
proach to modeling and segmenting the cardiac cavity in 3-D is
to use the contour already segmented to locate the contour in
the next slice or the next time point. Chenuoune et al. [50] use
the previous frame as the prior incorporated in a level set (Sec-
tion 3.2) technique. In the rst step, the endocardial border of
SAX cine MR images are segmented based on a level set method.
The previous contour is then registered using morphology opera-
tors to the next frame as a shape prior. Using the previous contour
can decrease the computation but can cause local minima problem
as well.
3.1.1.3. Learned shape. Another method uses a learned shape de-
rived from a training step with manually delineated images. Tsai
et al. [28] used a shape prior computed by applying Principal Com-
ponent Analysis (PCA) to a collection of signed distance represen-
tations of manually segmented data. Subsequently, the shape
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 971
Table 1
Statistical Methods: Shape prior, Active Shape Models and Active Appearance Models.
Method category Reference Modality/dimension/scanner Output Description Validation (# of Data)
Shape based
(Shape Prior,
ASM)
Koikkalainen et al. [23] Cine MR, 3D, Siemens Vision/
Sonata
+Epi + RV A set of different methods 3D human (20), EB
Suinesiaputra et al. [24] Cine MR, 2D, Philips Gyroscan +Epi ICA decomposition 3D Human (N:44, P:45),
EB
OBrian et al. [25] Cine MR, 3D, GE Genesis Signa +Epi PCA, contour coupling for
unseen contour
3D Human (33), EB
van Assen et al. [26] Cine MR, 3D, Philips Gyroscan +Epi Fuzzy feature detection 3D Human, EB
Lorenzo-Valds et al. [27] Cine MR, 3D, Siemens Sonata +Epi + RV EM incorporated in ASM 3D Human, EB
Tsai et al. [28] Cine MR, 3D, N/A +Epi Shape prior and level set 2D Human (1), EB
Sanchez-Ortiz et al. [29] Echo,3D, Philips Sonos 7500 endo Phase-based acoustic
feature detection
3D Human (9), EF
compared by SPECT
MUGA
Jacob et al. [30] Echo, 2D, Philips Hewlett
Packard SONOS 5500
endo Dynamic Snake Model 2D Human (N:4, P:5), EB
Esther Leung et al. [31] Echo, 2D, Philips Sonos 7500 endo Shape Model applied to
the invisible regions
3D Human (35), EB
Song et al. [32] Echo, 2D, +Epi Gradient direction
feature
2D Human (N:29, P:45),
EB
Lorenz and von Berg [33] CT, 3D, Philips Brilliance +Epi + RV + A Deformable mesh 3D Human (27), EB
van Rikxoort et al. [34] CT, 2D endo Atlas model 3D Human (29), EB
Frangi et al. [22] Cine MR, 3D, Philips PoweTrak
6000
+Epi B-spline registration 3D Human, EB
Peters et al. [35] CT/ Cine MR Epi + RV + A + V Distance to the model 3D Human CT (28) &
MR(42), EB
Zhou [36] Echo, 2D, Multivendor endo Shape regression
machine
2D Human (527 four CH),
EB
Schaerer et al. [37] Cine MR, 3D +Epi Newton dynamic law and
elasticity as energy
3D Human (15), EB
Makela et al. [38] PET/ Cine MR, 3D, Siemens
Magnetom, Siemens ECAT
+Epi + RV Intensity, edge and
elasticity energies
3D Human (10), EB
Tobon-Gomez et al. [39] SPECT, 2D +Epi Mahalanobis distance 3D Human (20),
simulation, Phantom, EB
Ma et al. [40] Echo, 3D endo Distance to the model 3D Human (P: 28), Cine,
EB
Hoogendoorn et al. [41] CT, 3D, Toshiba Aquilion Epi + RV + A + V Bilinear shape model 3D Human (45), EB
Codero-Grande et al. [42] Cine MR, 3D, GE Genesis +Epi MRF 3D Human (43), EB
zmc et al. [43] Cine MR, 2D, PhilisGyroscan +Epi A-priori search space 3D Human (N:2, P:18), EB
Lee et al. [44] Cine MRI,2D, GE Signa +Epi Circular shape prior 3D Human (38), EB
Stalidis et al. [45] Cine MR, 4D, +Epi NN based shape model 3D Human (32), EB
Dietenbeck et al. [46] Echo, 2D, GE vivid E9, Toshiba
Powerstation 6000
+Epi Thickness term 2D Human (20), EB
Ben Ayed et al. [47] Cine MR, 2D endo Overlap prior 3D Human (20), EB
Ayed et al. [48] Cine MR, 2D +Epi Max-ow, Distance to a
shape
3D Human (20), EB
Grbic et al. [49] CT, 3D Valve boundary Constrained multi-linear
shape model
3D Human, EB
Chenuoune et al. [50] Cine MRI, 3D, Siemens
Symphony
endo Geometry matching using
the previous frame
3D Human (N:7, P: 11),
Tagged MR
Folkesson et al. [51] Contrast MR, 2D, GE Signa CV/
i
+Epi Local Hessian features 3D Human (11), EB
Andreopoulos and Tsotsos
[52]
Cine MR, GE Signa +Epi 2D + T ASM 3D Human (33), EB
Pluempitiwiriyawej et al.
[53]
Cine MR, 2D, Brucker AVANCE
DRX 4.7 T
S + EPI + RV 5 DOF ellipsoid shape
prior
3D Human (48), EB
Hansegrd et al. [54] Echo,3D, GE Vingmed Vivid 7 +Epi Independent AAM 3D Human (36), EB
Mitchel et al. [55] Cine MR, Echo, 3D, Philips
Gyroscan
+Epi PCA based 3D Human MR (56), 2D
Human echo (64), EB
Mitchel et al. [56] Cine MR, 3D +Epi + RV PCA based 3D Human (60), EB
Mansi et al. [57] Cine MR, 3D, Siemen Avanto/
Philips Achieva
RV growth prediction
in repaired TOF
Diffeomorphism 3D human (P:49), EB
Peyrat et al. [58] DT-MRI, 3D, GE CV/I Fiber direction model Diffusion tensor statistics 3D dog (9, ex vivo), 3D
human (1, ex vivo), EB
Isgum et al. [59] CT, 3D, Philips Mx8000 IDT +Epi + V Multiple Atlas, local
decision fusion
3D Human (29), EB
Carneiro et al. [60] Echo, 3D endo ANN (Deep Learning
Architecture)
3D Human (14
sequences), EB
AAM Zhang et al. [61] Cine MR, 4D, GE Signa +Epi + RV 4D heart model 3D TOF (25), 3D Human
(25), EB
Joint ASM/AAM Bosch et al. [62] Echo, 2D endo 2D AAM + motion 2D human (P:129 Four
CH), EB
Motion Models Lekadir et al. [63] Cine MR, 3D, Siemens Sonata endo Inter-landmark measure 3D Human (50), EB
Duchateau et al. [64] Echo, 2D, GE Vingmed +M Diffeomorphism by
logarithm of the ow
2D Human (N:21, P:14),
EB
972 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
prior was incorporated into a level set framework in order to seg-
ment cine MR images. Folkesson et al. [51] used the distance to a
prior shape in the context of a geometric active contour model
(Section 3.2). The prior was computed by training the algorithm
using a set of images. Instead of the image pixels, local features de-
rived by Hessian operator were utilized to increase the speed of the
algorithm. In [44], the heart model was constructed in the wavelet
domain and used as the prior. The wavelet transform was applied
Table 1 (continued)
Method category Reference Modality/dimension/scanner Output Description Validation (# of Data)
Paragios [65] Echo, Cine MR, 2D endo + M Level set + learned shape-
motion prior
2D Human
Dydenco et al. [66] Echo, 2D, GE Vingmed,
Toshiba Power Vision 6000
+Epi + M Regional statistics curve
evolution
2D Human, EB, TDI
Punithakumar et al. [67] Cine MR, 2D endo Cavity/myocardium
overlap prior
3D Human (20), EB
Feng et al. [68] PET, 3D +M Center of mass based
rigid registration
Simulated images,
phantom
Pednekar et al. [69] Cine MR, 2D +Epi Motion map of the frames 3D Human (N:8, P:6), EB
Myronenco and Song [70] Echo, 3D +M Motion coherence by
temporal regularization
3D Human, EB
The output is classied as endocardium only (endo), epicardium (+Epi), RV (+RV), Atria (+A), great vessels (+V), Tag lines (+tag) and motion (+M). The magnetic eld is 1.5T
unless specied. Some elds are missing, incomplete or unclear in the original papers and are thus left blank. EB: Expert Based, N: Normal, P: Patient, SM: sonomicrometry,
TOF: Tetralogy of Fallot (a type of congenital heart disease). Since any segmentation method delineating the epicardium or the RV also delineates the endocardium, the key
(endo) is used for methods that only segment the endocardium.
Table 2
Deformable/level set methods: This table classies the articles that are based on deformable model or level set.
Method category Authors Modality/dimension/scanner Output Description Validation (# of Data)
Deformable model
and level set
Angelini et al.
[102]
Echo, 3D, Philips iE 33 endo + RV Level set, Mumford-Shah
function
3D Human (10), EB, EF
(compared to cine MR)
Sarti et al.
[104]
Echo, 2D endo Level set, Rayleigh model 2D Human (15), EB
Wolf et al.
[105]
Echo, 3D, Philips Sonos 7500 endo Feature detection using
edges
3D Human (N:14, P:10), EB
Jolly et al.
[106]
Cine MRI, CT, 2D, Siemens Magnetom MR/
Siemens Somatom CT
+Epi Distance to the shape prior 3D human (MR:29, CT:18), EB
Hautvast et al.
[107]
Cine MR, 2D, Philps Gyroscan Intera S + Epi + RV Distance to the shape 2D Human (69 SAX, 38 LAX),
EB
Lynch et al.
[108]
Cine MRI, N/A, 2D S + Epi Probabilistic shape prior 3D Human (4), EB
Zhu et al. [109] Cine MR, 3D, GE Signa +Epi 4D shape model 3D Dog (32) & Human (22), EB
Lin et al. [110] Echo,2D, Philips Sonos 7500 endo Probabilistic shape prior
and level set
2D Human, EB
Chen et al.
[111]
Tagged MR, 2D, Siemens Trio 3T Tag
lines + M + Epi
Feature detection using
Gabor
3D Human (N:6, P:11),
Phantom
Chen et al.
[112]
Tagged MR, 3D +tag lines + M MRF Human SPAMM data
Debreuve et al.
[113]
SPECT endo Local features Simulated images
Zagrodsky
et al. [114]
Echo, 3D, Philps Sonos 7500 endo Gradient Vector Flow,
Deformable mesh
3D Human (10), EB
Montagnat
et al. [115]
SPECT, 3D, +Epi Distance to a mesh,
newtons dynamic law
3D Human, EB
Verres et al.
[116]
Cine MR, 3D, Siemens +Epi FE, Hyperelastic warping 3D Human (1), Simulated
images
Phatak et al.
[117]
Cine MR,3D, Siemens Avanto +Epi Fiber, Hyperelastic warping 3D Human (1)
Fang et al.
[118]
Echo, 2D, Yale online database endo GMM 2D Human (N/A), EB
Barbosa et al.
[119]
CT, Echo, 3D, GE vivid 7 endo B-spline 3D Human, EB
Rougon et al.
[120]
Tagged MR, 2D, GE +Epi + M Gradient ow of MI 3D Human (N:12), Simulated
images
Kermani et al.
[121]
Cine MR, 3D +Epi Active mesh model 3D Human, Simulated images
Huang et al.
[122]
Cine MR, 2D endo Metamorph:
texture + shape
2D human, EB
Kaus et al.
[123]
Cine MRI, 3D, Philips +Epi Deformable contour 3D Human (121), EB
The output is classied as endocardium only (endo), epicardium (+Epi), RV (+RV), Atria (+A), great vessels (+V), Tag lines (+tag) and motion (+M). The magnetic eld is 1.5T
unless specied. Some elds are missing, incomplete or unclear in the original papers and are thus left blank. N: Normal, P: Patient, EB: Expert Based, SM: sonomicrometry,
since any segmentation method delineating the epicardium or the RV also delineates the endocardium, the key (endo) is used for methods that only segment the
endocardium.
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 973
to the cardiac surfaces in the spatiotemporal domain to extract the
coefcients. A neural network model was generated to combine
the local and global information in order to extract the trained
shape and segment the cardiac boundaries. The Fourier decompo-
sition approach was shown to be able to represent different shapes
by their Fourier descriptors. Coarse shape coefcients were com-
puted by low-order harmonics, while higher order coefcients rep-
resented the ne detail.
3.1.1.4. Thickness term. Practically, the endocardial and epicardial
contour segmentations may overlap due to variable contrast and
haziness of the boundaries. This problem dramatically increases
the error and leads to unrealistic rendered 3D heart images. In or-
der to tackle this problem, Dietenbeck et al. [46] used a constraint
that poses a forced distance between the endocardial and epicar-
dial contours. The thickness constraint was combined in a level
set framework in addition to a regional intensity term and a dis-
tance term describing the distance of the contour to a learned
shape. This technique was applied to echocardiography images to
segment the LV epicardium and endocardium simultaneously.
3.1.1.5. Other statistical shape prior techniques. Ben Ayed et al. [47]
proposed to compute the endocardial and epicardial contours
simultaneously using the rst frame. In the rst step, three image
region classes were proposed: 1. LV cavity containing blood; 2.
Myocardium; 3. Background containing adipose tissue, lungs, etc.
The algorithm assumes that the overlap between the kernel-based
intensity distributions within each region remain the same
through the consecutive frames. The Bhattacharyya coefcient
was used as the overlap measure. The Bhattacharyya coefcient
is a popular measure to determine the overlap between two statis-
tical samples. This coefcient is generally used to calculate the rel-
ative closeness of the two distributed classes. In a novel approach,
the energy term does not assume that the overlap between the
intensity proles within different regions has to be absolutely min-
imal. This modication helps to include the Papillary Muscle as
well. The authors were able to achieve competitive results without
using geometric training or preprocessing which leads to higher
exibility in the real clinical setting.
Ben Ayed et al. [48] proposed to use combined energy terms
consisting of the distance to a learned shape in addition to an
intensity-matching constraint. The rst cardiac frame was utilized
for training of the model of the histogram. The algorithm was ap-
plied to cine cardiac images for segmentation of the epicardial
and endocardial boundaries in cine MR SAX images. The prominent
advantage of the last two articles is reduction of the training time.
Since training is only based on the rst frame, the training time is
signicantly reduced. As a disadvantage, the validation is based on
20 datasets. Increasing the number of the tests set can increase the
reliability of the method.
Codero-Grande et al. [42] coarsely delineate the myocardium
initially. The tissue statistics is modeled using Gaussian Mixture
Model (GMM) according to the intensity and gradient of the LV
contour and the tissue inside the LV. GMM tries to model the tissue
histogram using a weighted summation of Gaussian distributions.
Consequently, a center-surround biannular radii is overlaid on the
Table 3
Biophysical methods: This class of techniques is based on the physical priors of the human heart.
Method
category
Authors Modality/dimension/
scanner
Output Description Validation (# of Data)
Biophysical
models
Bistoquet et al. [124] Cine MR, 3D, Philips
Intera
+Epi + RV Deterministic incompressible model 3D Human, Tagged MR, EB
Bistoquet et al. [125] Cine MR, 3D, Philips
Intera
+Epi + RV Deterministic nearly incompressible model 3D Human (N:3, P:3),
Tagged MR, EB
Garson et al. [126] US, 3D, Visual Sonic
Vevo 770
+Epi Deterministic incompressible model, Gradient
Vector Flow
3D mouse, Simulation
Zhu et al. (MIA) [127] Echo, 3D, Philips iE 33 +Epi Statistical nearly incompressible (Gaussian
assumption), level set
3D Dog (11) & Human (22),
EB
Papademeteris et al.
[128]
Echo, 3D, HP Sonos
5500
+Epi Fiber direction 3D Dog (N;2, P:2), SM
Sermesant et al.
(2003) [129]
SPECT, DTI MR, Philips +Epi + RV + M Fiber direction 3D human, EB
Bachner et al.
[130,131]
Echo, 2D +M Fiber direction 2D Human, Simulation,
phantom
Hu et al. [132] Tagged MR, 3D +Epi + RV + M Fiber direction, FEM 3D Human, Dog
Fan et al. [133] CT, 3D, N/A Endo Newton dynamic model for local force 3D Dog (N:16)
Sermesant et al.
(2006) [134]
Cine MR, 3D, Philips +Epi + RV + M Mass-Spring model, Fiber direction 3D Human, EB
Wong et al. [135] Cine MR, 3D, N/A +Epi + RV + M physiome model 3D Human, EB
Klein et al. [136] PET, 2D +M FEM Phantom
Yan et al. [137] Cine MR, Echo, 3D,
Philips 7500
+Epi + M FEM 3D Human, Implanted
marker
Remm et al. [138] Cine MR, 3D, Siemens
Vision
+Epi + M FEM 3D Human (13), Tagged MR
Shi et al. [139] Cine MR, 3D +M FEM 3D Human, Implanted
marker
Sinusas et al. [140] Cine MR, 3D, GE Signa +Epi FEM 3D Dog (8), Implanted
markers
Szilgyi et al. [141] Cine MR & CT, 3D +Epi + M Electromechanical model 3D Human (42)
Papademetris et al.
[142,143]
Cine MR, 3D +Epi + M Linear elastic model 3D Human, Implanted
marker
Klein et al. [144] PET, 3D +M Linear elastic model 3D Human (1), Phantom
Gigengack et al. [145] PET, 3D +M Hyper-elastic model, mass preservation Simulation, phantom, 3D
Human (21)
The output is classied as endocardium only (endo), epicardium (+Epi), RV (+RV), Atria (+A), great vessels (+V), Tag lines (+tag) and motion (+M). The magnetic eld is 1.5T
unless specied. Some elds are missing, incomplete or unclear in the original papers and are thus left blank. N: Normal, P: Patient, EB: Expert Based, SM: sonomicrometry,
since any segmentation method delineating the epicardium or the RV also delineates the endocardium, the key (endo) is used for methods that only segment the
endocardium.
974 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
circular myocardium of SAX slices. Thereafter, a 3D polar grid is
generated on the images. A Markov Random Field (MRF) system
including the prior and the likelihood terms is dened over that
grid. A Markov random eld is a graphical model of a set of
memoryless random variables represented by an undirected graph
that works similar to a Bayesian network. The intensity and the
gradient likelihood over different image subsets are constructed
using the previous grid and nally the parameters of the MRF are
recursively estimated and used for segmentation of cine MR
images.
3.1.2. ASM
The intensity, probability, and estimated contours from previ-
ous spatial and temporal locations may not represent the cardiac
boundaries well; this is especially true in cardiac US images since
at times, the contours are not complete and the cavity cannot be
fully visualized. The main advantage of the ASM methods is their
ability to overcome the noisy structure and drop outs of the cardiac
images based on probabilistic knowledge of the object which is
independent of the intensity [13,14]. ASM builds a whole shape
model using manually segmented data. Subsequently, the model
is registered on the images as will be discussed. A shape model is
dened as a structure which reects the typical structure of a spe-
cial set of anatomical objects of interest; i.e., the shape model is
invariant to transformations. There are several ways to represent
a shape: 1. cloud point, 2. surface, 3. mesh/triangulation (a set of
points with connectivity), 4. skeletonization, 5. parameterization
via a set of basis functions such as B-spline or NURBS. In computa-
tional cardiac studies, surface and mesh models are utilized more
frequently. Since most Active Shape Models have the same general
structure, below, the ASM is discussed in general terms and the dif-
ferences among the methods are described. Basically, there are ve
steps in use of ASM for segmentation:
1. Contour extraction and spatial alignment: A database containing
adequate number of examples is manually segmented in the
training phase. Several landmarks are selected on the contours
of the manually segmented training set. Subsequently, the
detected landmarks are aligned to a dened coordinate using
rigid registration techniques such as the Procrustes method
[71]. One shape is arbitrarily selected as the reference.
This step is usually the same in most papers but some variations
exist. Lekadir et al. [63] used inter-landmark measure as an invari-
Table 4
Non-rigid registration methods using basis functions. In this section basis functions such as B-spline are utilized to model the cardiac surfaces and motion.
Method category Authors Modality/dimension/scanner Output Description Validation (# of Data)
Non-rigid registration
using basis function
Amini et al.
[152,153]
Tagged MR, 2D +tag + M B-splines snake 3D Human (5), Simulated
images
Redeva et al.
[154]
Tagged MR, 3D +Epi + tag + M B-splines snake 3D Human, Simulated
images
Huang et al.
[155]
Tagged MR, 4D +Epi + tag + M B-splines snake 3D Human, Simulated
images
Tustison et al.,
2003 [156]
Tagged MR, 3D, Siemens Sonata +Epi + RV 3D B-spline FFD 3D Dog, simulated images
Tustison and
Amini [157]
Tagged MR, 4D, Siemens Sonata +Epi + RV + tag + M NURBS biventricular model 3D Dog, Simulated images
Deng and
Denney [158]
Tagged MR, 3D +Epi + tag + M B-splines registration 3D Human (10), Simulated
images
Chandrashekara
et al. [159]
Tagged MR, 3D, Siemens Sonata +Epi + tag + M FFD 3D Human (12), EB
Lin et al. [160] Cine MR, 2D +Epi + tag + M B-spline 3D Human, EB
Sundar et al.
[161]
Cine MR, 3D, Siemens Sonata +Epi + tag + M Cubic spline 3D Human (3), Tagged MR
Perperidis et al.
[162]
Cine MR, 3D, 7T (GE Excite
Console, magnex Magnet), Epic
12.4
+Epi B-spline registration 3D mouse, EB
Ledesma et al.
[163]
Echo, 2D, Siemens ACUSON +M B-spline 2D Human (N:6, p:6),
Simulated images
Ledesma et al.
[164166]
Echo, 2D +M B-spline 2D Human, Simulated
images, TDI
Elen et al. [167] Echo, 3D, GE Vingmed +M Elastic registration 3D Human (N:3, P:1),
Simulated images
Chen and Guan
[168]
MR, 3D +Epi + RV NURBS 3D Human
Metz et al. [169] CT, 3D +M B-spline FFD 3D lung and heart
Zheng et al.
[170]
CT, 3D +Epi + A + V Thin Plate Spline 3D Human
De Craene et al.
[171]
Echo, 3D, GE Vivid 7 +Epi Diffeomorphic B-Spline FFD 3D Human (N:9, P:13)
Peyrat et al.,
2010 [172]
CT, 4D +Epi,+RV,+M Diffeomorphic demon 3D Human, post RF-ablation
data, Simulated images,
Suhling et al.
[173]
Echo, 2D +M B-spline moments, Optical
ow
2D Dog (6), Simulated
images, Phantom
Yue et al. [174] Echo (intracardiac), 2D, Model
Ultra ICE, Bos ton Scientic
+M Maximum Likelihood, Spline
based control points
2D Dog (4), SM
Zhuang et al.
[79]
Cine MR, 3D, Philips +Epi + RV + A Locally Afne Registration,
Adaptive Control Point status
3D Human (37)
The output is classied as endocardium only (endo), epicardium (+Epi), RV (+RV), Atria (+A), great vessels (+V), Tag lines (+tag) and motion (+M). The magnetic eld is 1.5T
unless specied. Some elds are missing, incomplete or unclear in the original papers and are thus left blank. N: Normal, P: Patient, EB: Expert Based, SM: sonomicrometry,
since any segmentation method delineating the epicardium or the RV also delineates the endocardium, the key (endo) is used for methods that only segment the
endocardium.
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 975
ant shape representation that allows the decomposition of the glo-
bal prior as well as constraining each individual landmark. The in-
ter-landmark measures rely on barycentric coordinates based on
three coefcients to describe the relative position of each landmark
with respect to two neighbor triangles of different shapes and
poses. The barycentric coordinate system is a homogeneous coor-
dinate system in which the location of each point is represented
with respect to the center of mass, or the barycenter. The authors
suggested that inter-landmarks carry larger proportion of the
shape difference with respect to the other and this leads to inaccu-
rate alignment.
2. Temporal alignment: Different datasets have different numbers
of frames. In that case, an interpolation (such as spline or bilin-
ear) in time is necessary in order to make the number of frames
similar in the temporal direction [57,60]. Here again one dataset
is arbitrarily selected as the reference.
3. Construction of the shape model: A set of selected points distrib-
uted on the surface known as PDM (point distribution model)
can be formulated as:
x x
1
; y
1
; z
1
; . . . ; x
n
; y
n
; z
n

T
1
Each 3D shape data has a surface and a particular PDM distributed
over the surface. The key is that the PDMs for data in the training
database should have anatomical correspondence. Probability
shape models try to derive a statistical map of these points in the
form of mean x and covariance S of the PDM as:

x
1
N

N
i1
x
i
2
S
1
N 1

N
i1
x
i


xx
i


x
T
3
4. Dimensionality reduction: Dimensionality reduction of the train-
ing set is usually performed by using Principal Component
Analysis (PCA) to nd a small set of values that best represent
the observed variation. PCA extracts the eigenvalue decomposi-
tion of the covariance matrix, providing the principal eigenvec-
tors. Principal eigenvectors show the variability in the data. In
practice, the eigenvalues that describe 9599% of the total var-
iance are kept and the rest are discarded. Subsequently, each
shape may be represented as:
x

x ub 4
where u is the selected eigenvectors and b is the vector of shape
parameters.
Instead of the above-mentioned linear equation, Hoogendoorn
et al. [41] used a bilinear model to segment the ventricles, atria
and great vessels in CT images. In the bilinear mode, an additional
parameter (b) was added to provide a better model of the point set.
The bilinear model represented an extension of the linear model by
using two factors (A and b) while removing each factor leads to a
linear model. The bilinear model is formulated as:
x A
T
Wb 5
where X is a scalar observation dened by the point set, A and b are
parameterization vectors, and Wis similar to the eigenvalue matrix
PCA is based on the assumption that the data are Gaussian dis-
tributed which may not be true. To cope with this problem, some
authors have used Independent Component Analysis (ICA) [72]
which assumes statistical independence [24,43]. ICA is a technique
to separate set of data into additive non-Gaussian subcomponents
provided that the subcomponents are mutually statistically
independent. However, ICA increases the computational burden
in comparison to the PCA. Several other variants of PCA have been
developed in the literature. In [24], temporal dynamics and inter-
subject variation is tackled using Multilinear PCA (MPCA) and Mul-
tilinear ICA (MICA). Bosch et al. [62] performed the PCA technique
in smaller regions to give more local versatility to the general
shape model. Therefore, the local landmarks achieve regional inde-
pendence with regard to the global shape.
5. Shape correspondence: Shape correspondence computes the
transformation (T) that relates the object (x
0
) to the shape model
as:
x
0
T

x ub 6
This is the most important and distinctive part of statistical shape
modeling. Correspondence is performed by overlapping the statisti-
cal model on the test object (object to be segmented) and subse-
quently the transformation of the point sets that leads to the
maximal overlap is estimated. In the case of cardiac segmentation,
if the model contains both LV and RV, they can simultaneously be
modeled and segmented. It is noteworthy that the manual delinea-
tion is limited to the training step and the rst frame (in semi-auto-
matic techniques). Fully automatic techniques try to nd the image
correspondence without any initial contour.
Several techniques have been used for the correspondence of
the point sets. One of the major techniques is Iterative closest point
technique (ICP) [73]. ICP iteratively estimates the global transfor-
mation T and then applies that transformation (T) on the current
position of the point distribution. The transformation T is updated
based on the minimization of a least squares cost function that is
the distance between the expected point distribution position
and current estimate of image boundary points. In practice, ICP
consists of four steps: (1) using the nearest neighbor criteria to
map the points of the object to the points of the model, (2) Estimat-
ing transformation parameters applied to the point set (p
i,t
) based
on a minimizing the mean square cost function such that:
f T

m1
i0
kTp
i;t
p
i;t1
k
2
7
(3) Transforming the point set using the estimated parameters, (4)
the rst three steps iterates recursively until the cost function is less
than a small predened value [73].
However ICP is computationally costly and cannot handle dif-
ferent energy functions for correspondence computations. Opti-
mized matching techniques can be utilized instead of brute-force
point set matching. Non-rigid registration techniques such as B-
spline registration (described in Section 1.3.4) have also been used
for shape correspondence since they are inherently smooth and
can handle different energy functions. Besl and McKay [73] and
Frangi et al. [74] used the landmarks extracted from manually
delineated images to build a cardiac model. The landmarks were
propagated using volumetric B-spline registration due to several
advantages. B-spline non-rigid registration is less restrictive
regarding the structure which is due to the faster implementation
and inherently smooth nature of the spline basis functions. No
search space or point to point mapping is needed either. It is pos-
sible to achieve smooth results and handle multiple point set mod-
els at the same time. The B-spline registration will be discussed in
details later in this survey. In an additional article, Frangi et al. con-
structed an atlas of binary volumes based on quasi-afne registra-
tion using the Normalized Mutual Information (NMI) metric [75].
ASM and AAM are mostly used for segmentation purposes. Nev-
ertheless, since the correspondence among the point sets is com-
puted, the motion of the point set can be subsequently analyzed.
If the point set is positioned on the contours (endocardium or epi-
976 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
cardium), the derived motion will be sparse. However, the point set
could be positioned on the heart as a 3D mesh to cover the inside of
the myocardium in order to achieve a measure of dense motion.
3.1.2.1. Handling multiple objects or atlases. An Atlas can represent
one object or a set of normal or abnormal objects. Multi atlas prop-
agation and segmentation (MAPS) techniques have become popu-
lar recently in the eld of medical image segmentation [76,77].
MAPS combines object intensity and object label (contour) while
the intensity is used for registration and the label is used for the
propagation of the contours or the prior model. Modied versions
of MAPS are also proposed. MUPPS (MUltiple Path Propagation and
Segmentation) uses a set of atlases as well as a set of paths of prop-
agation similar to a multiple classier strategy [78]. The selection
of the optimal atlas and path is based on MI as the similarity crite-
rion. In similar work, Isgum et al. [59] argued that a single atlas
may not be a good representation of the whole population and pro-
posed a multi-Atlas model that uses decision fusion to select the
optimal atlas. In the rst step, an afne registration was used to
align the global image. Subsequently, nonrigid registration based
on B-spline was performed using a gradient descent technique.
MI was utilized as a measure of image matching. To cover the
whole range of transformation and in order to increase the speed
of the algorithm, multi-resolution and multi-grid strategies were
adopted. Finally, the atlas that gives the best registration success
is given an increased weight. The algorithm outperformed the sin-
gle best atlas strategy and averaged shape-atlas strategy.
Zhuang et al. [79] used LARM (Locally afned Registration
Method) to transform each substructure (LA, LV, RA, RV and ves-
sels) of the heart in a separate step. LARM was able to provide an
initial registration of the images to align the cardiac subcompo-
nents. In order to rene the registration, FFD registration was used
in the next step. The novel aspect proposed by the authors in this
step was Adaptive Control Point Status (ACPS) that turns the con-
trol point status of the object on or off based on the performance
of the registration. The status of the control points was updated
adaptively to guarantee that the active control points were not
inactivated. The proposed technique was able to overcome the
shape complexity of the heart in cardiac MR images by decompos-
ing the problem into several smaller structures and was able to
achieve a better computational speed.
In order to handle different structures such as ventricles and at-
ria more efciently, multiple-shape model and piecewise registra-
tion methods have been proposed. Instead of a single global shape
model, van Rikxoort et al. [34] used multiple shape models that act
locally using a method called ALMAS (Adaptive Local Multi Atlas
Segmentation). Atlas is a point set model that represents an ana-
tomic structure. ALMAS nds the number of necessary atlases to
efciently reconstruct the cardiac model. It locally and automati-
cally selects the most appropriate atlases u
i
(S
i
) to make the nal
combined atlas (S). In ALMAS, n registrations (T
i
) are applied to dif-
ferent atlases such that:
S
1
n

N
i1
u
i
S
i
8
The method was applied to cardiac CT images to segment the ven-
tricles and atria and great vessels in 3D. It was shown that the mul-
tiple-shape model provides more local autonomy in the atlas.
Ecabert et al. [80] developed a model-based approach for the seg-
mentation of the four chambers and great vessels using 3D CT
images. Hough transform was applied rst to automatically localize
the heart. ASM was utilized to construct the cardiac model from
coarse to ne scales using PCA dimensionality reduction. Piecewise
afne transformation was used to handle the shape variability and
match the model to the objects. The shape model was adjusted by
changing the degrees-of-freedom of the allowed deformations. To
ensure that the mesh remains continuous in-between the cham-
bers, a weight was assigned to each local model. The user can also
manually change the continuity as well.
3.1.2.2. Handling incomplete objects. Esther-Leung et al. [31] pro-
posed two different methods (model-driven and edge-driven) for
tracking the myocardium in echocardiography images. The ap-
proach was motivated by the fact that in echocardiography, visibil-
ity of the myocardium depends on the view. The technique relied
on a local data-driven tracker using optical ow (a temporal regis-
tration technique that for the most part uses the intensity con-
stancy assumption between corresponding pixels in successive
frames [81,82]) applied to the visible parts and a global statistical
model applied to the invisible parts of the myocardium. It was con-
cluded that the shape model can handle the invisible tissue in
ultrasound images as well as the missing boundaries. Another
shape based tackling of drop outs in echocardiography images
was described in Zhou [36]. The authors use Shape Regression Ma-
chine (SRM) as a method to overcome the fuzzy boundaries in 2D
echocardiography images without using the initial delineation. The
SRM uses statistics of the shape, appearance, and anatomy in the
training step to construct a model. Subsequently an automatic ini-
tialization was derived using a rigid shape. The initial contour is
updated using a nonlinear regressor to directly associate the non-
rigid shape with the image appearance.
3.1.2.3. Training volume size considerations. The number of datasets
in the training set should be large enough to cover different types
of diseases and dysfunctions. Any undertrained shape model can
theoretically lead to false results and over-tting [83]. In the case
of 3D and 4D shape modeling; very large datasets are needed, lead-
ing to the curse of dimensionality. Therefore, the extracted heart
model may be unable to cover different cardiac morphometrics.
Zhang et al. [61] used the manual segmentation of the rst frame
of the test dataset as an adjunct to the shape model to overcome
the limited training dataset problem. Koikkalainen et al. [23] de-
scribed several methods to articially increase the size of the data-
base using different techniques such as nonrigid movement and
combination of Principal Component Analysis (PCA) and Finite Ele-
ment Model (FEM). In a separate work, Ltjnen et al. [84] pro-
posed several methods to generate synthetic training data to
increase the size of the training dataset. Andreopoulos and Tsotsos
[52] argued that ASMs are unable to rely on a small training set to
capture the full range of biological shape variability. They handled
the problem of training 3D ASM through use of wavelets. Wavelets
can decompose the data into several sub-bands having different
amount of detail. Intuitively, wavelets can discard unnecessary de-
tails of the manually segmented boundary and keep the coarse and
stable parts. The technique was performed in four steps: (1) the ob-
ject was aligned to the shape model; (2) 2D wavelet was performed
in two steps on the coarse band and thus leaved seven image
bands; (3) the shape model was constructed in the wavelet domain
based on the coefcients of the wavelet transform; (4) inverse
wavelet transform was used to recover the shape in the space
domain.
3.1.2.4. Extension to the temporal dimension. The incorporation of
temporal data can be tricky due to the different resolutions of
the time dimension, higher variation of the motion, and computa-
tional expense. Extension of ASMs temporal modeling has been
performed in [52,62].
3.1.2.5. Diffeomorphism. One of the limitations of most image regis-
tration techniques is lack of explicit constraints to ensure that the
computed transformation is invertible. Folding of the grid over
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 977
itself can lead to the corruption of the neighboring structures of the
model or triangular ipping [85]. Therefore, diffeomorphic tech-
niques are of interest due to the smooth invertible transformations
with smooth inverse solutions. Since diffeomorphism has been al-
most exclusively used in the context of ASM in the cardiac segmen-
tation and registration eld, it is categorized in this section.
Diffeomorphic registration algorithms [8688] guarantee an
invertible continuous differentiable mapping between the object
features in order to preserve the topology and orientation of the
anatomical structures over time. The log transform of the motion
eld was incorporated in the shape model to conserve homeomor-
phism in [60] since the logarithmic transform can decrease the va-
lue of the motion. In another work, Beg et al. proposed a variational
diffeomorphic model based on cardiac ber elements in DT MRI
cardiac images of postmortem biopsies [76].
3.1.2.6. Shape variability. The differences in the anatomic variability
of the heart originate from three sources: (1) subject variability
due to the heart motion; (2) inter-subject variability due to the
shape differences among different humans; (3) pathological vari-
ability due to the abnormal cardiac size or function. In order to
overcome this problem, some authors have proposed combined in-
ter and intra-subject atlases that considers the huge shape varia-
tion of the heart [48].
3.1.2.7. Drawbacks of ASM. The probabilistic knowledge is usually
derived from a training step. This method mandates a comprehen-
sive database, tedious human effort, and high clinical and technical
expertise. The adequate size of the training set that includes differ-
ent pathologies can be a huge problem. This problem can be cum-
bersome since the cardiac chambers can vary widely in size and
motion, especially if uncommon diseases are also considered. The
learned template is limited to recognize a specic group of images
with similar properties and may miss others. Different training
steps should be used for each echocardiography or MR imaging
view in 2D techniques. Additionally, the traditional shape model
is a global structure while local landmarks do not have self auton-
omy to t to the local edges. ASM requires good initialization as
well. If the point distribution set is large, the computational time
can also be problematic in ASM [55,56].
3.1.3. AAM
Active Appearance Models use the same platform and steps of
ASMs but include the texture (intensity variations) appearance
of the object as well. The object intensity or gradient perpendicular
to the boundaries is usually considered as the appearance texture.
The shape data (s) and the appearance data (g) are combined to
make a joint linear system as:
x x /
shape
W
shape
Q
shape
c
g g /
Appear
Q
appear
c
9
where /
shape
and /
Appear
are independent eigenvectors of shape and
appearance, W
shape
is a diagonal weight matrix, Q
shape
and Q
Appear
are
the eigenvector matrices of the combined shape and appearance
and c is the combined shape appearance parameter vector. The ob-
ject data normal to the boundary contour (also known as prole)
are mainly computed by interpolation of the intensity or intensity
gradients in the direction of the contour normal [8992]. It is shown
that the normalization of the prole leads to more accurate results.
Two methods are linear normalization using an initial offset [89]
and non-linear normalization [62] to handle non-Gaussian
distributions.
Different object proles can be computed using several other
techniques such as Gabor lters [93], gradient strength and direc-
tion [8083], regional features [94], color features [95] and combi-
nation of several proles [96]. In another work, Song et al. [32]
used pixel feature vector as a combination of the smoothed inten-
sity values and the second directional derivative to construct the
shape model.
3.1.3.1. Advantages and drawbacks of AAM. ASM is faster and
achieves more accurate local point location than the AAM, but
the AAM also models the texture. Since the internal structure of
the heart is taken into account, memory problems can be a big is-
sue especially in 3D and 4D AAM methods. Decomposing the large
matrix into a smaller one is a preliminary solution. Decreasing the
resolution [55,62] and sparse regional analysis of the prole [94]
were proposed as well.
3.1.4. Motion models
The heart has an approximately periodic motion that is congru-
ent in space and time. Each region of the heart moves on a more or
less periodic curve called regional motion trajectory [2,3]. Motion
trajectories can be used as diagnostic tools in medical imaging.
The motion trajectories relevant to a region should be congruent
in time and make an almost closed path. There are several strate-
gies to make the motion smooth such as shape-motion models,
Kalman lters, and Markovian systems. Motion prior is a model
that can simulate the spatial and temporal changes of the displace-
ments by taking the motion pattern of the cardiac cycle into ac-
count as an additional constraint. Several papers that have
considered motion models are reviewed in this section.
Dydenco et al. [66] applied a level set algorithm which made
use of shape and motion prior, for both segmentation and tracking
of echocardiographic images. The method is based on three steps:
(1) the trained shape is aligned to the image using a rigid registra-
tion technique; (2) the aligned shape is used as an initial contour
for the level set method. The level set uses the data from the
learned shape prior and the statistics of the inside and outside of
the evolving curve to update the endocardial and epicardial bor-
ders; (3) the evolution of the level set is used to train the motion
prior.
Paragios [65] embedded a motion prior and a shape prior in a
level set function. The motion prior minimized the sum of absolute
difference of the corresponding images in the time dimension. The
prior shape was based on distances of the point set to a model. The
distribution of the distances was assumed to be Gaussian. Puni-
thakumar et al. [67] proposed to minimize an energy function con-
sisting of the distance of the transformed shape to a prior shape (a
trained shape) as the geometric constraint. A graph cut distribution
method was utilized in the minimization of the energy function
and delineation of the LV cavity in cardiac MR images. Since a sin-
gle Markovian cannot handle the complex heart motion, a set of
weighted models were combined together to handle the different
types of motion of the heart. The multiple model system was able
to automatically switch between the models and identify the
appropriate multiple model that matches the cardiac motion based
on a training process. Finally the technique was applied to the cine
MR SAX images for the segmentation of endocardial shapes as well
as to dene the trajectories in time through different frames.
Myronenco and Song [70] developed the Coherent Point Drift
(CPD) technique, constraining the motion of the point set in the
temporal direction for both rigid and nonrigid point set registra-
tion. The point set distribution was modeled with a Gaussian Mix-
ture Model (GMM). The GMM centroids were updated coherently
in a global pattern using maximumlikelihood to preserve the topo-
logical structure of the point sets. The algorithm was used for both
rigid and non-rigid applications. In the nonrigid case, the motion
coherence constraint was added based on regularization of the dis-
placement elds. The purpose of regularization is to increase the
motion smoothness. The motion is dened to be smoother if it
978 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
oscillates less which means that it has less energy at high frequen-
cies. The method was applied to 3D echo images of the LV in order
to compute displacements.
3.2. Deformable models
3.2.1. Parametric active contours
Deformable models, or active contours (also known as snakes)
technique which was rst described by Kass et al. [97], is a popular
physically inspired, model-driven technique based on parametric
curves, surfaces or volumes, that deform under internal and exter-
nal forces. The external energy forces the contour to move toward
the image data (such as an edge). The internal energy controls the
contour based on a regularizing smoothness constraint. Additional
energy terms can constrain the deformable model to achieve better
results. The general deformable model energy function can be writ-
ten as:
E E
ext
E
int
10
External energy is usually dened as:
E
ext
krjG
r
x; y Ix; yjk
2
11
where G
r
(x, y) is a two dimensional Gaussian function with stan-
dard deviation r and I(x, y) is the intensity at point v(s) = [x(s), y(s)].
Internal energy is dened as
E
int

1
2
askv
s
sk
2
bskv
ss
sk
2
12
where a and b are weights, the rst order term (membrane term:
kv
s
(s)k
2
) denes the stretching and the second order term (thin-
plate term: kv
ss
(s)k
2
) denes the curvature.
This energy function was minimized within a variational energy
minimization. The numerical optimization was improved by Amini
et al. [98] who cast the optimization within a dynamic program-
ming framework and introduced the concept of soft and hard con-
straints. Further improvements to this framework was proposed by
Klein et al. who introduced DP B-spline snakes [99].
Some studies have incorporated other terms such as shape prior
and physical constraints as will be discussed later. Deformable
models have been widely used for the segmentation and tracking
of cardiac images in both MRI and echocardiographic images.
Since the edge map of the image can be misleading due to the
noise and missing data, GVF (gradient Vector Flow) was proposed
as a new external energy function to handle the edge function
smoothly. GVF is derived based on the minimization of the energy
function proposed in Eq. (13) where v is the Gradient Vector Flow,
l is the smoothing weight, rI is the image gradient, and krI
2
k
penalizes the edge information [100].
E
GVF

_ _
lkvk
2
krI
2
k kv rIk
2
13
3.2.2. Geometric active contours
Level-sets, rst introduced by Osher and Sethian [101], repre-
sents an implicit function which deforms based on regional inten-
sity or edge-based feature and is able to develop topological
changes. The initial contour at time zero (C
0
) corresponds to the
zero level set of the function /:
C
0
x; yj/x; y; 0 0g f 14
If we represent a continuous speed function as F then the general-
ized level set equation dynamics can be parameterized as:
/
t
Fjruj 0 15
where F represents the speed function for the curve evolution. The
speed function depends on internal properties such as geometry
(e.g. curvature) of the interface and external properties such as im-
age gradient. Given an initial contour (or contours), an implicit
function is dened and deformed at each pixel where the zero-level
set determines the actual position of the curve(s) as a function of
time. Level set approaches are stable but are computationally
costly. Deformable models are mostly used for segmentation tasks.
However, a measure of cardiac motion can be calculated by com-
puting the displacements of the contour or the mesh.
Table 2 describes the related articles using this class of tech-
niques [102123]. Angelini et al. [102] proposed a level set tech-
nique to segment Ultrasound echocardiography images. It is
benecial to describe the method utilized in this paper, since it
was based on Chan and Vese [103], which is a classical level
set algorithm that can be utilized for other purposes as well. The
authors minimized an energy function that contained area, length,
and intensity variations inside and outside a contour (the image is
considered piecewise smooth inside and outside the contour) such
that:
E aLcontour bVinsideofcontour c
_
X
jI
c
0
j
2
H/dXq
_
X
jI c
1
j
2
1 HudX 16
where a, b, c, q are the weighting parameters, I is the intensity, c
0
and c
1
represent a xed intensity level that represent the mean dis-
tribution of the intensity inside and outside the curve. H(/) is the
Heaviside function dened as:
Hu
1 u P0
0 u < 0
_
17
The length of the contour can be written as:
Lcontour
_
X
jrH/jdX
_
X
jr/jd/dX 18
where d(/) is the Dirac function and the area inside the contour can
be written as:
Ainsideof contour
_
X
jHujdX 19
The authors extended this method to delineate the endocardium of
both LV and RV cavities.
Sarti et al. [104] used the Rayleigh distribution of the speckle
statistics to segment cardiac US images in a level set framework.
The Rayleigh distribution is dened as:
pI
Raileigh
Ix; y=r
2
exp Ix; y
2
=2r
2
_ _
20
where r is the standard deviation. The authors assumed that the
intensity distribution of the tissue inside and outside the endocar-
dial curve is similar through the cardiac frames since they represent
the texture of the blood and the myocardium.
Barbosa et al. [119] developed a level set technique based on
the global intensity inside and outside of the object boundaries
and an additional local regional intensity term. The energy func-
tional was handled in spherical coordinates to match the anatomic
shape of the LV. The level-set was evolved based on B-spline con-
trol points to increase the smoothness of the curve evolution. It
was shown that the algorithm is able to effectively segment the
endocardium in echocardiography images. Wolf et al. [105] used
an energy function consisting of region-based information of sev-
eral landmarks in a deformable model framework combined with
morphology operators. The algorithm was used in order to seg-
ment the endocardium in 2D echocardiography images. These
aforementioned deformable methods are mostly based on the
intensity information that may cause errors. Additional techniques
and constraints are considered to resolve this problem. Huang et al.
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 979
incorporated the shape and interior texture into the variational
deformable model framework using a technique named metamor-
ph [122]. The object texture is modeled using a nonparametric ker-
nel-based approximation of the intensity probability density
function. The deformations that the model is modeled using cubic
B-spline based Free Form Deformations (Section 3.4). The model
deforms under the force of boundary and region based functions.
It is shown that the proposed metamorph model when applied to
cine MRI images can converge to a reasonable solution even when
initialized far away from the original object boundaries.
Kaus et al. [123] utilized a triangulated surface mesh that de-
forms in response to different energy forces. The shape model
was embedded into the deformable energy function by maximizing
the similarity of the distribution of the object mesh vertices. The
mesh surface was iteratively scaled and rotated based on a prior
as well as internal and external energy terms.
Zagrodsky et al. [114] utilized a deformable mesh technique
based on internal and external energies in order to segment 3D
echocardiography images. Montagnat et al. [115] proposed a 4D
deformable mesh driven by Lagrangian dynamics to extract the
epicardium and endocardium in Cine MR images. A simple motion
prior derived from the averaged contour trajectories was utilized
to compute the boundaries more accurately. Lin et al. [110] used
feature extraction using Gabor lters. Subsequently, a Robust Point
Matching (RPM) method was applied to the grid tag intersections
in different image frames to build a one-to-one correspondence
and to compute the motion. Rougon et al. [120] utilized general-
ized information measure a parameter derived from NMI to com-
pute the motion in tagged MRI. The authors made use of novel
information measures as a superset of both NMI and MI. Kermani
et al. [121] used a combination of elasticity and distance to a
learned mesh model in the context of Active Mesh Model (AMM)
to segment SAX cine MR images.
3.2.2.1. Advantages of deformable models. Deformable models can
be customized to match particular shapes by changing the
parameters of energy functions. There is no need for training
the model. They are able to generate smoothed closed parametric
or implicit curves or surfaces from the images. Finally, it is possi-
ble to integrate physical and shape prior constraints in developed
techniques.
3.2.2.2. Drawbacks of deformable models. The disadvantages are
inaccuracy in handling noisy images, and inability to cope with
specic protrusions/bifurcations. The basic snake energy alone is
not able to segment some objects and therefore modications
and extensions to the energy function are crucial to handle the
problems. They are also dependent on the parameters as well as
contour initialization. The disadvantage of level set techniques is
the vital importance of appropriate speed function to advance
the level set function.
3.3. Biophysical/mechanical models
This group of techniques relies on the mechanical, physical, or
physiological properties of the heart such as FEM, incompressibil-
ity of the myocardium, and physical or elasticity laws as con-
straints for segmentation and motion estimation of cardiac
images (Table 3 [124145]).
3.3.1. Finite Element Models for cardiac mechanics
The cardiac tissue can be divided into small nite elements that
move in accordance to the mechanical laws. As a basic model,
Hooks law of spring (F = k x; where F is the force, x is the dis-
placement, and k is the spring constant) can be extended for elastic
materials as:
r E e 21
where r is the stress (the force applied to the element), e is strain
(the element deformation with respect to the original length, Sec-
tion 4.1) and E is the elastic or Youngs modulus. For many materi-
als, Youngs modulus is approximately constant over a wide range
of strains. These materials are called linear elastic. Heart tissue is
non-linear and not linear elastic. This basic model however can be
modied using more complex models such as a hyperelastic model
that simulates a nonlinear relationship between the stress and
strain. Additionally, the stressstrain relationship is not the same
in different cardiac directions (anisotropic) due to the ber orienta-
tion of the cardiac tissue [146,147].
3.3.2. Isotropic cardiac mechanic models
Isotropic models consider the heart as a homogeneous medium.
Fan et al. [133] incorporated the regional force of the myocardium
by including Newtonian dynamics as an additional term in the
snake framework. The acceleration of each element of the cardiac
boundary is simulated by the second derivative of the displace-
ment as:

F
ext
S; t F
int
S; t m
d
2
S; t
dt
2
22
where F represents the snake energies, S is the cardiac boundary
element at time t and m represents the element mass. The tech-
nique was applied to canine 3D US echocardiography images in or-
der to segment the endocardium. Boundary Element Method (BEM)
proposed by Yan et al. [137] was a technique to place the B-spline
control points on the boundaries to estimate the dense motion
elds using GRPM. GRPM was applied to the LV point set based
on feature points extracted based on endocardial surface curva-
tures. 3D B-spline non rigid registration was used to extract the cor-
respondence. Since the structure of the heart is the same in all
modalities, the method was applied to analyze the cardiac function
from Ultrasound and cine MRI. Remme et al. [138] utilized a set of
ducial markers selected by the user, in an FEM model distributed
over the cardiac geometry to compute the motion of the LV. The
motion of the ducial markers was used in order to prescribe defor-
mations for the model. The method was applied to tagged MR
images to segment the epicardium and compute the motion. Addi-
tionally, it was hypothesized that the algorithm can be extended to
analyze other modalities such as cardiac CT and echocardiography.
Shi et al. [139] combined the data from two different sources: cine
contour data and mid-wall phase contrast. The combined informa-
tion was used to extract the displacements based on an FEM
framework.
3.3.3. Incompressibility of the myocardium
The myocardium is believed to be nearly incompressible during
systole and diastole due to the high water content. Myocardial vol-
ume changes have been quantied during systole and diastole in
several studies such as Hamilton and Rompf [148], Bowman
et al. [149], and Hoffman et al. [150,151]. It is believed that the
myocardial volume (MV) is relatively constant during a cardiac cy-
cle, varying about 3.55%. The conservation of volume of the myo-
cardium has been utilized as an additional term in several articles.
The small compressibility of the heart is usually attributed to the
compressible blood vessel lumens and the difference in the total
volume of blood in the myocardium depending on the phase of
the cardiac cycle. Bistoquet et al. [124] utilized Normalized Mutual
Information (NMI) in addition to the incompressibility of the myo-
cardium using a curvilinear coordinate system which is based on
the mid-wall surface of the LV wall. The cardiac contour was man-
ually segmented in the rst frame of cine MR images. To achieve
the new coordinate system, the authors reparameterized each
980 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
point inside the myocardium with respect to the mid-wall hyper-
plane of the heart by using a sign distance equation normal to
the mid-wall surface. Subsequently, NMI was used to update the
control points located on the cardiac contour and the incompress-
ibility criterion was incorporated in the contour evolution frame-
work as a prior. In another work, the authors argued that the
incompressibility condition has a failure rate of about 5% and pro-
posed nearly incompressible model that allows a small change in
the myocardial volume by adding a small offset to the above-men-
tioned framework [125].
So far, we have only described contributions were the myocar-
dial incompressibility has been simulated deterministically. Sta-
tistical simulation of the incompressibility has also been used.
Zhu et al. [127] incorporate the speckle statistics and myocardial
volume incompressibility using probability models. The com-
pressibility (q) is statistically modeled as a Gaussian (G(V
0
, r))
such that:
q/
in
; /
out

1

2p
p
r
exp
V V
0

2
2r
2
_ _
23
where the volume of space between the endocardium (/
in
) and epi-
cardium (/
out
) is the myocardial volume and r
0

1
120
V
0
. This simu-
lation allowed about 5% variation in the myocardial volume. Speckle
statistics can be initially classied as pre-Rayleigh, Rayleigh, and
post-Rayleigh, depending on the density and spatial distribution
of the scatterers. The most popular model considers a large number
of random scatterers which produces Rayleigh distribution leading
to full speckle formation. Pre-Rayleigh pattern occurs when the
number of scatters is not large enough. Post-Rayleigh pattern occurs
when the scatterers are not randomly distributed but have a general
periodic pattern due to the tissue structure. Other statistical models
that can handle the three different situations have been proposed
such as Nakagami and Rician distribution. In the aforementioned
article, the tissue statistics are separately modeled using Nakagami
distribution in three different media (l = 3): 1. Blood pool, 2. Myo-
cardium, 3. Peripheral tissue. The data terms are dened as:
log pIj/
in
; /
out

3
l1
logp
l
I dx 24
Zhu et al. then combine the speckle statistical model and the incom-
pressibility model in a level set framework in order to segment the
cardiac endocardium and epicardium in 3D echocardiography
images.
3.3.4. Fiber direction
Myocardial bers are tangential at the endocardium and epicar-
dium, and at mid-wall follow a right handed helical geometry. The
heart contracts in the direction of the cardiac bers and therefore
taking the mechanics of cardiac bers and ber directions into ac-
count may lead to more accurate results. Diffusion Tensor (DT) MRI
is able to dene the myocardial ber directions. Normal canine
DTMRI data is available online and may be included as part of
the myocardial model (www.ccbm.jhu.edu/research/DTMR-
IDS.php). However the ber directions should be registered on
the cardiac model. Furthermore, it is known that ber directions
become disorganized and change during disease.
Fiber direction models can be simplied or complex. Bachner-
Hinenzon et al. [130] divided the myocardial tissue into three in-
ner, mid and outer sections. Wavelet transform was applied to
each section separately in order to model the different ber orien-
tation in the cardiac wall. Papademetris et al. [142,143] modeled
the LV myocardium as a linear elastic structure dened by
mechanical parameters such as Poissons ratio and Youngs modu-
lus. To simulate the anisotropic propagation of force through the
myocardial wall, the continuous myocardial ber twisting and ori-
entation were modeled using FEM. Sermesant et al. [134] used a
FEM biomechanical deformable model integrating the internal
and external energy as well as the ber direction for segmentation
and motion estimation from cine MR cardiac images. Internal en-
ergy was modeled based on the linear elasticity of a Tensor-Mass
model. Finite Element Method was handled based on linear tetra-
hedral elements, mass-lumping model, and Newtonian differential
equations using an explicit time integration scheme. Fiber direc-
tions were obtained according to the DTI images in order to orient
the elemental directions. External energy force directions were
computed on the surface nodes of the model as vectors orthogonal
to the surface of each element and the external force values were
made proportional to distance to the model point. The algorithm
was used to segment the LV epicardium and endocardium and
RV in SPECT and cine MR images. Additionally, since the correspon-
dence among the cardiac elements is known, a measure of motion
may be derived as well. Verres et al. and Phatak et al. [116,117]
used hyperelastic warping in addition to the ber direction infor-
mation in a deformable framework. The epicardial and endocardial
surfaces of the end diastolic MR images were rst segmented by a
user. The triangulated myocardial surfaces were utilized as the ba-
sic structure in a FEM preprocessing software in order to build a
hexahedral volume. A transversely isotropic hyperelastic model
was utilized to simulate the myocardium. The ber directions were
estimated using three different ber direction models for different
cardiac segments as: (1) Fiber direction varying from 90 at the
epicardium to + 90 at the endocardium for the basal level, (2) heli-
cal pattern for the inner and outer layers: The inner layer varies
from +90 to 0 from the basal level to the apical level and the out-
er layer varied from +90 to 0 from the basal level to the apical le-
vel, and (3) ber directions at the basal septal and apical levels are
aligned with the measurements from DTMRI data from dog and
human cadaver hearts. Hu et al. [132] proposed a biventricular
model for LV and RV that includes the ber direction of the myo-
cardium as well. Subsequently, the elements of FEM were distrib-
uted on the model to simulate the stressstrain relationship.
Expectation Maximization was used to solve the model and com-
pute the cardiac contours and motion from tagged MR images.
3.3.5. Electromechanical models
The cardiac periodic motion originates from the electrophysio-
logical activity of the heart. The main trigger of the cardiac elec-
trical activity is located in the sinus node. The sinus node
generates the leading depolarization wave that propagates to
the atria and ventricles. The electrical wave causes the myocardial
bers to contract and produces the mechanical contraction of the
heart. Wong et al. [135] used a combination of electrical wave
propagation model and electromechanical coupling model in
addition to the biomechanical heart model to extract the bound-
aries in 3D cine MR images. The authors proposed a mesh-free
framework to solve for this integrated model. Every node was gi-
ven an inuence domain and the value of each point of the model
was computed by summing the effect of the inuence regions. Fi-
nally, a least square technique was applied to solve for the inte-
grated model.
Biophysical models have been widely used for the registration
and motion detection of the cardiac images. The physical priors
such as incompressibility or ber direction can be useful in deter-
mining cardiac displacements. Biophysical models have the
advantage of providing additional constraints based on the phys-
ical properties of the cardiac tissue. Additionally, training is not
necessary. However, the physical laws are not completely true;
as an instance the cardiac tissue is neither linear elastic nor hy-
per-elastic.
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 981
3.4. Non-rigid registration using basis functions
This class of techniques attempts to extract the non-rigid mo-
tion of anatomical objects using a set of basis function such as
splines that have inherent smoothness properties (Table 4 [152
174]). B-spline based representation of the tag planes in 3D were
used to track the myocardial motion in Amini et al. [152,153]. Red-
eva et al. [154] proposed an approach to nonrigid registration of
cardiac tagged MRI volumes with volumetric B-splines. The ap-
proach was extended to 4D in [155]. The smooth nature of the B-
spline basis functions lead to more congruent results. Rueckert
et al. [175] and Chandrashekara et al. [159] used a two-step regis-
tration technique: 1. Global registration using afne registration, 2.
Local registration using a spline based similarity matching. The
similarity function can be different measures such as NMI and
SSD. The advantage of B-spline based Free Form Deformation is
that it offers the capability to be used as a multimodal algorithm
to provide dense and pixel-wise results.
The basic idea of B-spline FFD is to transform an object by
manipulating an underlying spline-based mesh of control points U.
The resulting transformation denes the shape of the 3D object.
The energy term that leads the motion of the control points usually
consists of the similarity function and a spatial velocity smooth-
ness constraint but can be extended to any functional.
Tx; y; z

3
l0

3
m0

3
n0
B
l
uB
m
uB
n
uU
il;jm;kn
25
where T is the transformation and
i bx=n
x
c 1; j by=n
y
c 1; k bz=n
z
c 1 26
u x=n
x
bx=n
x
c; v y=n
y
by=n
y
c; w z=n
z
bz=n
z
c
where n
x
, n
x
and n
x
dene the number of control points in x, y and z
directions. B
l
is the lth basis function for the uniform non-rational
case is dened below for order up to cubic:
B
0
u 1 u
3
=6; B
1
u 3u
3
6u
2
4=6; B
2
u
3u
3
3u
2
3u 1=6; B
3
u u
3
=6 27
A similar 3D B-spline method was used in Deng and Denney [158].
The authors apply the 3D B-spline basis function in the cylindrical
coordinate system. The cylindrical axes are adopted to t to the
LV contour to simulate the anatomy of the heart during motion esti-
mation. The displacement smoothness is applied to the circumfer-
ential, radial, and longitudinal directions as an additional energy
term. Sundar et al. [161] dene a cardiac attribute vector at each
voxel as a feature that can be tracked during the cardiac motion.
The cardiac attribute reects the underlying cardiac structure at dif-
ferent scales. Each attribute vector includes the image intensity, im-
age boundary, and geometric moment invariants (GMIs). GMI is
computed at different image scales as thirteen rotation invariants
that are calculated from the zero-order, second-order, and third-or-
der 3D regular moments. Finally, the attributes are registered using
cubic B-spline registration. Tustison and Amini [157] and Lin et al.
[160] transform the Cartesian grid of control points in B-spline non-
rigid registration to a cylindrical lattice. This can be considered an
anatomical modication of the Cartesian grid to achieve better re-
sults. Declerck et al. [176] used a mathematical framework for
non-rigid registration of SPECT images by tting planispheric hy-
per-planes to epicardium and endocardium. The correspondence
between the cardiac contours is computed using ICP. The advantage
of using non-Cartesian coordinates is the symmetric structure of the
cardiac model which resembles the circular or cylindrical shape of
the heart as well. The disadvantages of the non-Cartesian system
are higher computation and the possibility of additional error dur-
ing the Cartesian-polar conversion especially near the poles of the
model.
Metz et al. [169] utilize a 4D (3D + time) free-form B-spline
deformation model based on a similarity metric that minimizes
the intensity variations over time. A public domain software (elas-
tix) was used for the elastic registration. The proposed method was
applied to both heart and lung 3D CT images. De Craene et al. pro-
pose Temporal Diffeomorphic Free Form Deformation (TDFFD) by
incorporating image similarity according to the sum of squared dif-
ferences, incompressibility, and a regularization term in a 4D B-
spline framework. Thin-plate-spline (TPS) is subsequently used to
warp the initial mesh towards the rened control points in the cor-
respondence step. The algorithm is applied to segment the 3D hu-
man echocardiography images. In [156,157] a biventricular cardiac
model is generated in both cylindrical-Cartesian and cylindrical-
polar coordinates to track the heart motion by using tag positions
in LAX and SAX MR images. Tag lines are parameterized based on
NURBS (Non-Uniform Rational B-Spline) basis functions. Chen
and Guan [168] also implemented a NURBS based model in a cylin-
drical coordinate system to segment the LV contour in cine MR
images. A volumetric NURBS object can be formulated as:
Sx; y; z

3
l0

3
m0

3
n0
B
l
uB
m
uB
n
uw
l;m;n
U
l;m;n

3
l0

3
m0

3
n0
B
l
uB
m
uB
n
uw
l;m;n
28
where w
l,m,n
is the assigned weight of each control point. NURBS
registration is an extension of the B-spline registration using addi-
tional weights. NURBS has an extra degree of freedom to adopt
the regional weight of the control points. It can handle sharp sur-
faces by increasing the weight of the attributed control points. Suh-
ling et al. [173] combine rigid registration in the optical ow
framework in order to detect the motion of 2D echocardiography
images. B-spline moments were applied to echo images to achieve
invariance to the translation and rotation. The algorithm is applied
to the B-spline moments of the image instead of the image intensity
in a coarse to ne strategy. The algorithm was validated using open
chested dogs after ligation of a coronary artery. Additional valida-
tions are based on simulation and phantom images.
Ellen et al. used elastic registration on 3D B-mode echocardiog-
raphy images to extract the motion and strain values. The method
was validated using simulated and real echo images [167]. Peyrat
et al. [172] decoupled the image registration in CT images into
two components: 4D spatial registration that dealt with the regis-
tration of the cardiac physical points; and 4D temporal registration
that dealt with the physiologic (systolic/diastolic) alignment of the
frames. The second component handled the trajectory modeling in
time over the cardiac cycle. The spatial registration was performed
initially and thereafter the temporal registration was computed.
Diffeomorphic Demons [177] were used as the registration tech-
nique. Demon technique uses a diffusion-like model to align two
images minimizing the intensity differences between the model
elements.
The advantages of the basis function based techniques (such as
spline) are their inherent smoothness and their ability to reduction
of the computation to control points. Additionally no training is
needed and the same framework can be extended for other appli-
cations. The disadvantages of such a framework are the depen-
dence of the results on the nature of the basis functions, number
of control points, as well as their position. The optimization tech-
nique may not lead to the best results if the control points do
not properly cover the complex portions of the shape, e.g., with
intrusions and protrusions. Table 5 summarizes the advantages
and disadvantages of each technique.
982 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
4. Validations
Manual tracking: Manual tracking of the markers has been uti-
lized for the validation of motion detection algorithms. However
manual validation is trickier in registration with respect to seg-
mentation. Manual landmark detection is cumbersome in 3D and
marker displacements do not represent sub-pixel motion. Finally
prominent landmarks are not a good sample of the general tissue
displacement because they usually represent edges, corners or
higher amount of contrast.
Simulation and phantoms: Several authors [158,163,167] have
tried to model the medical imaging techniques and generate a
set of simulated series. The importance of the simulator is to pro-
vide a set of images for which the ground truth is known. The
drawback of the simulated images is that it is not possible to per-
fectly model the imaging physics and acquisition. Phantoms [136]
can provide realistic images but it is difcult to have a dense
ground truth for phantom images.
Comparison to the other modalities: Several other validation
techniques have been used for cardiac registration such as compar-
ison with Tagged MR [124,125] and TDI [165]. Other modalities
provide an independent and objective validation of the algorithms.
However, pixel to pixel inter-modality comparison may need reg-
istration because the two images will not fully overlap on each
other. Comparison of different segments of the heart instead of pix-
el to pixel comparison can overcome this problem.
Implanted markers and sensors: Comparison of the implanted
markers is an independent though invasive validation. Several
authors have used inserted landmarks so far. Implanting sensors
such as sonomicrometry is another approach to validate the car-
diac motion. Sonomicrometry is the application of microcrystals
(small piezoelectric with the size of a few millimeters) embedded
on the myocardial surface. Ultrasound pulse is utilized to measure
the distance between the microcrystals based on the speed of
sound. An electric pulse sent to each crystal will be transformed
into sound wave, which passes through the medium to the other
crystal and is converted into an electric signal again. The distance
between the crystals can be calculated from this time of ight of
the received pulses. SM can provide independent and accurate
measurements but it is not possible to use the ultrasonic micro-
crystals simultaneously with the echocardiography machine due
to the interaction of the ultrasonic pulses. Therefore the measure-
ments should be performed separately which may cause unreli-
ability. In general implanted markers and sensors are invasive
and the local injury around the implanted sensor can change the
natural motion. Sonomicrometry measurements have been used
in [128].
Validation of the computed EF: Cardiac segmentation has been
usually validated using manual delineation of the in vivo images.
Since EF is calculated using the segmentation results, comparison
of the computed EF with the EF derived using other modalities
can be helpful. Ma et al. compared the LV mass extracted based
on the echocardiography segmentation with the LV mass derived
from cine MRI data [40]. Nuclear medicine techniques can provide
very accurate EF measures [2,3]. Sanchez-Ortis et al. have
compared the EF extracted by segmentation to the EF derived from
SPECT [29].
In-vivo validations: The in vivo validations are mostly performed
on humans, open chest dogs (before and after synthetic infarction)
and mouse. Synthetic infarction is able to evaluate the motion
detection techniques in analyzing the abnormal tissue motion be-
fore and after the pathology.
4.1. Computational outputs
Some techniques are multi-modal and can be extended to both
cine MR and echocardiography modalities [110,137,142,143,138].
Delineation of the endocardium is a common output in all the seg-
mentation articles. Epicardium is also segmented in some papers.
As mentioned before, errors are usually larger for the epicardium
and RV contours. Some papers have reported segmenting all the
ventricles and atria; see for example, Ltjnen et al. [84].
Strain is an index of deformation or lengthening or shortening
of an object. Strain and strain rate imaging allow the measurement
of regional myocardial deformation to assess specic local and glo-
bal functions. Strain measures deformation while strain rate is the
rate of the change of the deformation. Both of these measures have
been shown to provide complementary information about the clin-
ical assessment of cardiac function, Strain (s) is dened in one
dimension as:
S
1
2
l
l
0
_ _
2
1
_ _
29
where l and l
0
are secondary and original length of a line element in
the material and S is the nal measured strain. Strain rate (SR) is de-
ned as the velocity of strain changes such that:
SR
Straint
2
Straint
1

t
2
t
1

30
If I is the identity matrix, the Lagrangian strain tensor can be de-
rived as:
E
1
2
F
T
F I 31
where the elements of the deformation gradient tensor, F, are:
F
@x
@X
@x
@Y
@x
@Z
@y
@X
@y
@Y
@y
@Z
@z
@X
@z
@Y
@z
@Z
_
_
_
_
_
_ 32
While x = X + V(X), X represents the spatial coordinates in the unde-
formed coordinates, and V(X) is the motion vector at the corre-
sponding spatial location.
The Eulerian strain tensor, G, is:
G
1
2
I F
T
F
1
_ _
33
Diagonalization of the strain tensors will yield principal strain val-
ues and directions that describe the maximum and minimum val-
ues and directions for the deformation [157].
Table 5
summary of the advantages and disadvantages of the cardiac segmentation and registration methods based on shape modeling.
Method Advantage Disadvantage
Statistical Intensity-independent Training is needed, large database
Deformable model and level set Matching specic shapes and energy functions, versatility Dependence on parameters, sensitive to noise
Biophysical models Intensity-independent, no training Violations of the physical assumption, Dependence on
parameters
Non-rigid registration using basis
functions
Smoothness, potential to be used for a variety of modalities and
objects, no training
Convergence issues, Dependence on parameters
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 983
Regional analysis is usually performed on 17 American Heart
Association (AHA) prescribed segments of the heart. Fig. 7 shows
the different segments. The acronyms stand for antero-septal
(AS), anterior (A), lateral (L), posterior (P), inferior (I), and infe-
ro-septal (IS). For a review of topics related to determination of
strain from cardiac images, the reader is referred to
[156,157,178,179].
4.2. Numerical validation
Comparison of the validations of different studies is difcult
and intractable due to the different data sets, imaging views, seg-
mental analysis, and evaluation measures. Some papers have pro-
vided local segmental analysis of the 17 segments while other
results are reported as global functional parameters EF% error or
LV mass error. Clinical validations using sensitivity, specicity,
and p-value are utilized as well [61]. Occasionally the reports are
based on some of the cardiac segments. However, in general, the
surface distance errors such as Point to surface distance (p2s) or
MAD (Mean Absolute Difference) are mostly utilized. These mea-
sures are usually in the range of 13 mm for 2D/3D CT, MR, and
echocardiography images. Zhu et al. [109] have presented MAD er-
rors ranging from 1.11 to 1.33 mm for epicardium and 0.47 to
0.82 mm for endocardium depending on the cardiac segment.
The apical results are usually the worst while the mid LV results
are the best as intuitively expected. The error is higher for the RV
and epicardium with respect to endocardium [61,109]. Table 6 cat-
egorizes the articles that utilized the same evaluation metrics.
However, the numerical values are dependent on the database
and the way the data is used for the validation. Some studies dis-
carded the apical slices during the validation because it is cumber-
some to even manually delineate the apical segments.
4.3. Future directions
Thanks to the advances in image acquisition hardware and
instrumentation, the cardiac imaging eld is seeing rapid progress
and expansion. 2D cardiac imaging suffers from out-of-plane error
and limited reliability in obtaining appropriate cardiac planes in
sequential acquisitions. 3D imaging techniques such as 3D echo-
cardiography, MRI, SPECT, and cardiac CT are likely to partly re-
place the routine use of 2D imaging for accurate measurement of
cardiac size, function, perfusion, and metabolism.
Increased resolution of the 3D echocardiography images has
led to better analysis of the local and global LV function. With
developments in the multi-detector row CT technologies (more
Table 6
Numerical results of the cardiac modeling techniques. The articles that utilized the same metrics are compared in this table. However, the numerical values are dependent on the
database and the way the data are used for the validation.
Method Epicardium error (mm) LV endocardium
error (mm)
RV contour
error (mm)
EF% LA contour
error (mm)
RA contour
Error (mm)
MRI Mitchell et al. (2001) 1.75 0.83 1.71 0.82 2.46 1.39
Mitchell et al. (2002) 2.63 0.76 2.75 0.86
Lelieveldt et al. (2001) 0.77 0.74 0.63 0.65
Mitchell et al. (2002) 2.63 0.76 2.75 0.86
zmc et al. (2006) 1.77 0.57 1.86 0.59
Lynch et al. (2006) 1.31 1.86 0.69 0.88
Lynch et al. (2006b) 1.83 1.85 0.76 1.09
van Assen et al. (2006) 2.23 0.46 1.97 0.54
Lorenzo-Valds et al. (2004) 2.99 2.65 2.21 2.22 2.89 2.56
Ltjnen et al. (2004) 2.77 0.49 2.01 0.31 2.37 0.5
Hautvast et al. (2006) 1.84 1.04 2.23 1.10 2.02 1.21
Jolly et al. (2009) 2.91 2.48
Zhang et al. (2010) 1.67 0.3 1.81 0.4 2.13 0.39
Constantinides et al. (2009) 2.04 0.47 2.35 0.57
Jolly (2009) 2.26 0.59 1.97 0.48
Huang et al. 2.06 0.39 2.11 0.41
OBrien et al. (2009) 3.73 3.16
Sanchez Ortiz et al. 6.63 37
Stegmann et al. 0 3.0
Corsi et al. 2 5.5
Pednekar e al. 7.6 5.6
Codero Grande et al. 1.22 0.17 1.37 0.20
Zhang et al. 1.81 0.40 1.67 0.30 2.13 0.39
Kermani et al. 3.77 0.67
Peyrat et al. 3.10 2.08 Whole ventricular endo: 1.88 1.33
Zhuang et al. 1.69 1.60 1.06 1.02 1.50 1.51 1.69 1.68 1.51 1.62
Echo Ma et al. 12 9
Zhu et al. (TMI) 1.27 0.18 1.23 0.10
Zhu et al. (MIA) 1.7 0.52 1.4 0.28
Esther Leung et al. 1.19 0.47 1.4 6.7
Wolf et al. (2002) 3.44 1.18
Hansegard et al. (2007) 3.4 2.3
Lin et al. 1.64 0.5
Bosch et al. 3.54 1.62 0.66 5.5
Angelini et al. 4.6
Sarti et al. 1.6 1.8
0.86
CT Zheng et al. 1.21 1.41 1.13 0.55 1.55 0.38 1.32 0.42 1.57 0.48
Ecabert et al. 0.98 1.32 0.82 1.07 0.84 0.94 0.71 0.88 0.89 0.96
Isgum et al. Whole atlas error: from 0.7 0.17 to 0.89 0.07
984 V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989
detector rows, smaller detectors, etc.), have provided the capabil-
ity for acquisition of high quality 4D cardiac Images, preserving
the ne structural details inside the endocardium. The unseen
structures, such as trabeculation and cords can be visualized
and used by the clinicians [180]. With MRI, better gradient hard-
ware and RF coil technologies have resulted in high quality car-
diac imaging with better SNR and resolution, and at a higher
speed. Due to larger size of the resulting imaging data, for all
modalities, computer aided analysis methods are increasingly
mandated.
4.4. Challenges
Grand challenges in the eld of medical image processing are
held as a part of MICCAI (since 2009) and ISBI conferences (since
2012). They are able to produce unbiased validation of different
algorithms based on the same data set, thus eliminating the con-
founding character of patient type, vendor, and validation mea-
sures. However, the participant research groups are typically
limited to about 10 or less and therefore, most techniques are
not tested. Additionally, only a few challenges provide the data
for validation and comparison in the future publications. To date,
three grand challenges have taken place as a part of MICCAI
2009, 2011 and 2012.
1. MICCAI 2009, Cardiac MR Left Ventricle Segmentation Chal-
lenge: http://smial.sri.utoronto.ca/LV_Challenge/, This chal-
lenge has provided the data for future experiments and
maybe downloaded. The top ranked papers in this challenge
were Lu et al. [181] and Huang et al. [182]. Both papers include
a preprocessing and post processing stages similar to bottom-
up techniques. Lu et al.s technique [155] proposed using an
automatic roundness measure that locates the Left Ventricle.
Subsequently the epicardial contour was transformed from
Cartesian to polar coordinates. The nal contour was smoothed
using the Fourier transform. This method does not need user
interaction and provides the endocardial and epicardial con-
tours as well as the Papillary Muscle and trabeculation con-
tours. Huang et al. [182] utilized various features of cine MR
images and combined multiple image processing bottom-up
methods such as thresholding, edge detection, and morphology
operators in order to automatically segment the LV borders. A
deformable model was applied subsequently to the coarsely
processes images.
2. MICCAI 2011, The STACOM 2011 4D LV Segmentation Chal-
lenge: based on 100 cases for training and 100 cases for testing.
Data was subsequently removed and is not available for future
use. Website: http://www.cardiacatlas.org/web/guest/sta-
com2011 The MICCAI 2011 challenge was extended to cardiac
registration of Cine MR, 3D echocardiography and EP studies
and is based on about 16 MR and 16 3D echocardiography data:
The STACOM 2011 4D LV Segmentation/Registration/EP Sim-
ulation Challenge: (http://www.cardiacatlas.org/web/guest/sta-
com2011). The results of the challenge are not yet compared.
3. STACOM 2012 considered registration and segmentation meth-
ods based on simulation, phantom and patient data. The results
are not yet available to the public. http://www.miccai.org/
news/miccai-2012-workshops-and-challenges-call-papersAn-
other challenge was devoted to Coronary Artery Stenosis Detec-
tion and Quantication Evaluation Framework, Website: http://
coronary.bigr.nl/stenoses/
4.5. Helpful online resources
1. euHeartDB is a recent consortium of 16 different research insti-
tutes from six countries in Europe organized to improve the
diagnosis of cardiac diseases. The Euroheart database provides
a publicly accessible database to upload and download geomet-
rical models and software.
2. The cardiac Atlas project: http://www.cardiacatlas.org.
3. Available datasets and software:
1. York University cine MR dataset including the manual
segmentation of the endocardial and epicardial contours:
http://www.cse.yorku.ca/mridataset/.
2. Stegmann 2D data base: 14 set of annotated 2D Cardiac
cine MRI available at http://www2.imm.dtu.dk/pubdb/
views/publication_details.php?id=500.
3. Yale echocardiography atlas: http://www.yale.edu/
imaging.
4. CCBM available models/software/dataset: http://
www.ccbm.jhu.edu/software/index.php.
5. Graphical Interface for Medical Image Analysis and Simu-
lation: Available software developed in C for medical
image analysis applications, www.gimias.org.
6. SEGMENT: an open source software for the segmentation
of MR images: http://medviso.com/products/segment/.
7. RV growth model: An open source diffeomorphic model
for RV growth in children based on Matlab + data:
http://www-sop.inria.fr/asclepios/projects/Health-e-Child/
ShapeAnalysis/index.php.
8. Several heart models such as mean atlas, mean ber, and
tetrahedral mesh: http://team.inria.fr/asclepios/data/.
9. An open source code based on several algorithms such as
locally afne registration method (LARM), spatially
encoded mutual information (SEMI), as well as other
image/vector eld processing tools. (http://www.cs.ucl.a-
c.uk/staff/x.zhuang/zxhproj/index.html).
10. Several open source codes for rigid, afne, and nonlinear
registration: http://cmic.cs.ucl.ac.uk/home/software/.
11. ITK-SNAP: an open source extension of ITK for segmenta-
tion of medical images, http://www.itksnap.org/pmwiki/
pmwiki.php.
Fig. 7. Seventeen AHA prescribed segments for the heart (a) basal SAX view, (b) mid-LV SAX view, (c) apical SAX view. (antero-septal (AS), anterior (A), lateral (L), posterior
(P), inferior (I), and infero-septal (IS)) [156,157].
V. Tavakoli, A.A. Amini / Computer Vision and Image Understanding 117 (2013) 966989 985
5. Conclusions
This article presented a review summary of the shape modeling
applications to cardiac image analysis in MRI, CT, echocardiogra-
phy, PET and SPECT. The main classes surveyed were statistical
models, deformable models/level set, biophysical models, and
non-rigid registration techniques using basis function methods.
The article covered image analysis of cardiac images published in
journals within the last 10 years, classied in a number of tables
based on various properties such as method, modality, and valida-
tion techniques. Active shape and appearance models are widely
used for cardiac segmentation and registration. They are indepen-
dent of the intensity and can overcome confounding factors such as
the Papillary Muscle and contour fuzziness, especially in apical and
basal slices as well as echocardiography images. However, they are
dependent on an ofine and sometimes difcult training stage. Le-
vel set and deformable models do not need training and can adjust
to t different shapes. However, dependency on the initial contour
and parameters can be considered a drawback. Physical constraints
such as incompressibility of the myocardium, Newton law, and
FEM have been used as additional terms in this category. Basis
functions have been used as a technique to model the volumes
for cardiac segmentation and registration as well. Validation of
methods have primarily involved manual delineation and compar-
ison with the other modalities.
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