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Attenuation correction for PET/MR: Problems, novel

approaches and practical solutions
Axel Martinez-Möller ∗ , Stephan G. Nekolla
Nuklearmedizinische Klinik und Poliklinik der Technischen Universität München, Munich, Germany

Received 6 February 2012; accepted 8 August 2012

Abstract Die Schwächungskorrektur bei hybriden

PET/MR-Systemen: Probleme, neue Ansätze
Attenuation correction in PET is the primary prereq- und praktische Lösungen
uisite for quantification of the radiotracer’s signal.
Absolute quantification is the key to improve diagnostic
performance, to enable comparisons between follow-up Zusammenfassung
examinations and to perform pharmacokinetic modeling.
A large fraction of the 511 keV annihilation photons from Eine grundlegende Voraussetzung für die quantitative PET-
the positron emitters are scattered by the patient’s body. Bildgebung liegt in der erfolgreichen Schwächungskor-
Thus, they are discarded or do not even reach the PET rektur. Die Möglichkeit dieser absoluten Quantifizierung
detectors, while others are identified at the wrong loca- der Aufnahme von Radiopharmazeutika ist einer der
tion after being scattered. To account for these effects and primären Unterschiede zur der konventionellen nuk-
thus generate quantitative PET images showing the actual learmedizinischen Bildgebung. Erst damit ergibt sich
activity distribution, it is necessary to determine an atten- z.B. die Vergleichbarkeit serieller Untersuchungen und
uation map with the appropriate attenuation coefficients die Möglichkeit kinetischer Modellierungen physiologi-
for 511 keV photons at each voxel. In hybrid PET/CT sys- scher Prozesse. Die Schwächungskorrektur ist deswegen
tems, this is achieved using the information about the tissue von fundamentaler Bedeutung, da ein großer Anteil der
electron density provided by the CT and adjusting it for the 511 keV-Vernichtungsquanten aus dem Positronenzerfall
difference in photon energy. In PET/MR systems, there is im Körper des Patienten gestreut wird. Somit erreicht nur
no mechanism to directly measure the attenuation coef- ein Teil der Quanten die Detektoren oder wird durch die
ficients of the tissue. Determining the attenuation map in Streuablenkung falsch zugeordnet. Diese Prozesse kön-
PET/MR is an important challenge involving two problems: nen korrigiert werden, sofern die räumliche Verteilung
the determination of the patient’s attenuation map and des schwächenden Gewebes und dessen Schwächungsko-
the determination of the attenuation introduced by addi- effizienten bekannt sind. Im Fall eines anderen hybriden
tional hardware components. We describe the approaches Bildgebungsverfahrens – der PET/CT – misst man diese
investigated to deal with these problems and, based on Verteilung mit Hilfe des integrierten Computertomo-
the experience with a fully integrated PET/MR system, we graphen, wobei in guter Näherung nur Korrekturen für die

∗ Corresponding author: Axel Martinez-Möller, Nuklearmedizinische Klinik der Technischen Universität München, Ismaninger Str. 22, D-81675 München.

Tel.: +49-89-41402968; Fax: +49-89-41404950.

E-mail: (A. Martinez-Möller).

Z. Med. Phys. 22 (2012) 299–310
300 A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310

finally discuss potential solutions and limitations in a close unterschiedlichen Energien notwendig sind. In PET/MR-
to routine setting. Systemen stellt sich nun eine neue Herausforderung, da der
Kernspintomographie die Bestimmung der Röntgendichte
des Gewebes nicht zugänglich ist. Allerdings ist das nur
ein Aspekt, wenngleich ein sehr komplexer. Zusätzlich wer-
den die 511-keV-Quanten aber auch durch eine erhebliche
Menge messtechnisch notwendiger Komponenten des MR-
Gerätes geschwächt. Dieser Übersichtsartikel präsentiert
auf der einen Seite publizierte Lösungsvorschläge für diese
Probleme. Darüber hinaus werden aber auch – basierend
auf den ersten Erfahrungen mit einem vollständig inte-
grierten Ganzkörper-PET/MR-System – deren praktische
Umsetzung und Limitationen im routinenahen Betrieb

Keywords: PET/MR, Attenuation correction Schlüsselwörter: PET/MR, Schwächungskorrektur

Introduction When a 511 keV photon is scattered by the patient’s body,

it will not reach the detector which it would have reached if
Hybrid PET/MR scanners have recently been developed it would not have undergone the interaction (Fig. 1). This is
and many advantages compared to PET/CT and/or standalone known as photon attenuation, and reflects the fact that a line of
MR imaging are foreseen in several imaging scenarios [1–3]. response (LOR, defined as the line between two detectors) will
The manufacturers have proposed PET/MR scanners with two miss some of the photon pairs which were emitted along this
different architectures: sequential, such as the Philips Inge- line because of this interaction taking place for any of both
nuity TF PET/MR [4], and integrated, such as the Siemens photons. As an example, over 90% of the photon pairs for
Biograph mMR [5]. Both architectures share a common LORs going through the center of the abdomen are typically
aspect: the absence of a transmission system (rotating radionu- attenuated and missed by the detectors in their original LOR.
clide source as in standalone PET or CT as in PET/CT) in order
to estimate the attenuation map at 511 keV within the field of
However, PET imaging is severely affected by photon atten-
uation and scatter, and corrections are needed in order to
have quantitative images reflecting the true spatial distribu-
tion of the radiotracer. A prerequisite to these corrections is the
availability of an attenuation map containing the attenuation
coefficients for 511 keV photons at each voxel. The validity
of the PET images depends strongly on the accuracy of the
attenuation map. The determination of the attenuation map is
thus a major challenge for PET/MR [6,7] because MRI does
deliver signals which are in no way related to the attenuation
properties of tissue.
Here we first describe the physical concepts underlying
attenuation and scatter as well as the correction mecha-
nisms usually implemented in PET/CT scanners. Moreover,
we describe the different approaches proposed until now for
PET/MR and their implementation on commercially available

Attenuation and scattering of photons

The dominating interaction of PET annihilation photons
with human biological tissue is through Compton scattering, Figure 1. Diagram of a PET detector ring with two annihilation
whereas photoelectric absorption plays only a minor role. events demonstrating the effects of scatter (A) and attenuation (B).
A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310 301

Compton scattering introduces an additional problem: once caused by different respiratory states in each acquisition [9,10]
a scattered photon reaches a PET detector, the energy resolu- and artifacts introduced by the presence of metal [11] or iodi-
tion of the detector might not be good enough to determine nated contrast agents [12,13]. Furthermore, one must be aware
that the energy of the incoming photon was below 511 keV. that CT-based AC results in a higher radiation dose compared
If the other photon resulting from the same annihilation is to PET-based transmission scans.
also detected and accepted (with or without being scattered), In PET/MR systems, new approaches to provide the atten-
a coincidence event will be incorrectly assigned to the LOR uation map have been developed and will be described later
between both detectors; that is, we will observe photon pairs in this review.
along a LOR where they were not generated, an effect some-
what opposite to that of attenuation (Fig. 1). This effect is Scatter correction
often referred as scatter, and the ratio of accepted coinci-
dences which have undergone scatter to the total number of Scatter correction is used to estimate the number of scat-
accepted coincidences as scatter fraction. The scatter fraction tered coincidences which have been accepted by the detectors
in whole-body 3D imaging (without septa as found in most and subtract them. Different scatter correction techniques have
modern PET systems) is typically in the range of 30% - 50%. been investigated in the past, e.g. [14–21]. Currently most
whole-body scanners implement a single scatter simulation
Attenuation correction (SSS) [22–24], which estimates the scatter contribution based
on the emission data and the attenuation map by simulating
Attenuation correction (AC) is used to account for the back- exclusively the coincidences where only one of the photons
to-back photons emitted along an LOR and not detected (at has been scattered only once.
least not at this LOR) because they undergo Compton scatter- The SSS algorithm has been shown to be well suited for
ing. whole-body imaging, but its accuracy is compromised by the
As PET is based on the detection of coincident photons, scatter arising from annihilations outside the axial field of
the attenuation for events occurring within an LOR does not view (FoV) as well as by multiple scatter. Watson et al. [25]
depend on their location within the LOR, but only on the further refined the method to match the simulated data to the
total attenuation for this LOR. Accurate correction for photon measured data by including scale factors derived from the
attenuation in PET can thus be performed by multiplying the parts of the sinogram which correspond to the exterior of the
measured coincidences in each LOR by a factor specific to patient, segmented based on the data available in the ACF
each LOR, the so-called attenuation correction factor (ACF), sinogram. In this step, it is important that the attenuation map
which for a non-uniform attenuating medium can then be (and consequently the ACF sinogram) is not transaxially trun-
described as: cated. Otherwise, LORs assigned to the exterior of the patient
1  (because the attenuation map mistakenly shows air) might
ACFLOR =  = e LOR μ(x)dx actually pass through true activity causing the scale factors to
e LOR be too high; this effect is also sometimes observed in the case
The linear attenuation coefficient μ for 511 keV photons of motion between the emission data and the attenuation map
varies for biological tissues between below 0.03 cm-1 for the [26].
lung and well above 0.12 cm-1 for cortical bone.
Standalone PET, PET/CT and PET/MR systems use differ- Determination of the patient attenuation map
ent approaches to determine the ACFs. In stand-alone PET,
now nearly obsolete, the ACFs are typically measured with a We subdivide the determination of the attenuation map in
rotating radionuclide source (68 Ga/68 Ge or 137 Cs) by deter- PET/MR in two problems: the determination of the patient
mining the ratio between the number of photons detected with attenuation and the determination of the hardware attenuation
the imaged object in the scanner and the number of photons produced by other elements present in the FoV (patient bed,
detected in a blank scan. MR coils and occasionally other components such as ECG).
In PET/CT scanners, the CT data are used instead to Determination of the patient attenuation map in PET/MR is
determine the attenuation map containing the attenuation the most challenging problem. Three fundamental approaches
coefficient μ at each voxel, and the ACFs are computed by have been proposed until now, which we will further refer to as
integrating over each LOR. Because CT uses a polyenergetic segmentation-based, template-based and emission-based (see
beam at lower energies (approx. 60-140 keV for x-rays versus overview in Table 1).
511 keV in PET) the attenuation coefficients are adjusted by Segmentation-based approaches. The idea of segment-
means of a bilinear transformation [8]. CT-based AC offers ing the attenuation map in different tissue classes was already
many advantages as compared to transmission measurements proposed by Huang et al. in 1981 [27] in order to reduce
performed with rotating radionuclide sources, including faster noise propagation from the measured transmission images.
acquisition and reduced noise. However, it also presents new The method was improved with time and widely used on
challenges such as misregistration of the PET and CT data standalone PET scanners.
302 A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310

Table 1
Overview of the potential strengths of each MR-based attenuation correction method for whole-body imaging.
Ability to deal with

Speed Robustness Anatomical variations Bone Metal Limited MR FoV Patient-spec. ␮

Segment +++ +++ +++ + - - -

Atlas - + - ++ + + -
Emission + + +++ ++ ++ ++ ++
Note: reference potential values are provided, the performance and accuracy of each method may strongly vary depending on the particular implementation
and potential developments by future research (e.g. MR sequences allowing direct bone segmentation or faster implementations of the atlas and emission
based methods).

Figure 2. Results of an implementation of the segmentation-based approach using a UTE sequence to identify the skull for brain imaging,
reprinted by permission of the Society of Nuclear Medicine from Catana et al. [34]. (A) Attenuation maps obtained from segmentation of
3-tissue classes based on CT (left) and dual-echo ultrashort echo-time (DUTE) (right). (B) PET images reconstructed using CT-based (left)
and DUTE-based (middle) AC methods and image of the relative changes between the 2 methods (right).
A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310 303

Application of a segmentation-based approach for MR- specific contribution of bone. Steinberg et al. [39] and Schulz
based AC was first mentioned in the context of neurological et al. [40] proposed segmentation-based approaches using
imaging for standalone PET scanners [28–31], obviating instead T1-weighted turbo spin echo sequences, also ignoring
the need for time-consuming PET transmission images by the contribution by bone and allowing a faster acquisition at
spatially registering a segmented T1-weighted MR to the the expense of not differentiating between fat (␮=0.086 cm-1 )
PET emission data and applying the theoretical attenuation and soft tissue (␮=0.096 cm-1 ).
coefficients. Because cortical bone is hard to visualize in con- It should be noted that whole-body segmentation
ventional MRI sequences such as T1-weighted images [32], approaches represent an approximation of the true attenu-
it was then suggested to use technically rather demanding ation map and the performance depends on the number of
ultrashort echo time (UTE) MR acquisitions [33–35], which tissue classes considered [42,43]. The use of predefined atten-
facilitate the segmentation of the skull in the context of brain uation coefficients is a limitation which does not reflect the
imaging (Fig. 2). variability found in patients (e.g. different lung attenuation
Application of segmented MR-based AC for whole-body coefficients for different respiratory states). Furthermore, cur-
PET/MR imaging was first proposed by our group [36,37], rent segmentation-based approaches for whole-body imaging
using water-weighted and fat-weighted images derived from a ignore the contribution of bone, resulting in an underesti-
Dixon MR sequence [38] in order to classify each voxel as air, mation of the uptake for lesions located in the bone and its
lungs, fat and soft tissue (Fig. 3). Since bone cannot be robustly surroundings; different values for the underestimation of the
segmented in whole-body MR images, the method ignored the SUV of bone lesions have been reported by different groups:

Figure 3. Results from an implementation of the segmentation-based approach, reprinted by permission of the Society of Nuclear Medicine
from Martinez-Möller et al. [37]. On the top row, CT, CT-AC-PET and CT-AC-PET/CT images. On the bottom row, MR-based attenuation
map (within the dashed lines), MR-AC-PET and MR-AC-PET/CT images. The MR-derived attenuation map is created by assigning each
voxel of the MR data into air, lung, fat or soft tissue.
304 A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310

based on PET/CT data it has been estimated to be 5-15% Template-based approaches. A template-based approach
[37,40] or up to 23% [41], whereas simulations with the XCAT consists in matching a model to the patient’s anatomy, so that
phantom have led to a local bias of up to 17% [42] or even 30% the known attenuation map from the model can be applied to
[43]. In addition, the effect of MR contrast agents – while tech- the patient data. In early PET systems, such an approach was
nically not changing the water/fat separation – might influence sometimes used with simple models, first for brain studies
the image segmentation as they result in an increase of MR approximating the outline of the head to an ellipse on each
signal due to reduced T1 values. plane and later refined to automatically identify the body con-
Yet, segmentation-based methods are robust, computation- tour from the PET emission data [44–46]. For brain studies,
ally fast and the associated quantification error for bone the approach was further improved, proposing spatial registra-
lesions is repeatable and well understood. Therefore, com- tion of the SPECT data to a template derived from a digitized
mercially available PET/MR scanners are using this approach phantom [47] or registration of the PET data to a template
for MR-based AC: the Siemens Biograph mMR uses an adap- obtained by averaging scans of normal subjects [48].
tation of [37] while the Philips Ingenuity TF PET/MR uses an With the advent of the first PET/MR scanners, several
adaptation of [40]. groups proposed and evaluated the use of a template-based

Figure 4. Implementation and results of a template-based approach for brain imaging, reproduced from Schreibmann et al. [51] with
permission from AAPM. An atlas CT is non-rigidly registered to the acquired MR image, providing a synthetic CT matching the patient’s
A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310 305

approach for PET/MR brain imaging [48–52] (Fig. 4). The Emission-based approaches. The PET emission data can
approach was shown to be very successful. However, it be used to derive some information about the attenuation
required an accurate non-rigid spatial registration of the map. In fact, without the influence of scattered radiation,
acquired MR images and the template. This is feasible in the it would be possible based on the measured PET data to
head, but for whole-body imaging non-rigid registration has estimate both the distribution of radiotracer and the atten-
been reported to be error-prone [53]. Pure atlas-based meth- uation map (or at least the part relevant for the image
ods fail also in the presence of anatomical abnormalities (e.g. generation). This approach has been extensively investigated
amputation, lung tumor, etc.). Yet, by combining the template- for standalone PET imaging in order to obviate the need
based approach with information from the segmented MR and for a transmission measurement [55–61], but its success is
pattern recognition, the technical feasibility of the method was limited by the crosstalk between emission and attenuation
also demonstrated for whole-body imaging by Hofmann et al. data.
[54]. In PET/MR imaging, robustness is gained by using the
In summary, template-based approaches have shown a great segmented MR data as starting point. Nuyts et al. [62]
potential in the context of brain imaging, where the cortical described its application in order to recover truncated parts
bone from the skull can thus be robustly taken into account of the attenuation map (see subsection below) whereas
in the attenuation map. For whole-body imaging, template- Salomon et al. [63] reported that, using time-of-flight PET
based methods have the potential advantage of taking the bone data and an ideally segmented MR image, it might be
into account and partially recovering metal-induced artifacts, even possible to improve the MR-based attenuation map
being able to get closer to the real distribution of attenuation and assign proper attenuation values to the bones (Fig. 5).
coefficients than segmentation-based methods. However, this Defrise et al. [64] have further demonstrated that time-of-
comes at the expense of an increased computational time and flight PET data can lead to reasonable estimates of the
results which depend on the accuracy of a challenging non- attenuation map (up to a constant) even without a prior
rigid image registration. segmentation.

Figure 5. Results from an implementation of the emission-based technique, reprinted by permission of IEEE from Salomon et al. [63].
From left to right: T1-weighted MR image, segmented label map (each segment gets an attenuation factor), initial attenuation estimate and
estimated attenuation after 12 iterations.
306 A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310

Possible artifacts and limitations. The determination of Research reports regarding the presence of metal in MR-
the patient attenuation map faces two additional challenges: based AC are still scarce. Metal artifacts produce a severe
the limited transaxial field of view in MRI and the occasional local reduction or even elimination of signal in the MR image,
presence of metal. which might result in underestimation of the attenuation fac-
There is often transaxial truncation in the MR images due tor and produce negative artifacts (decreased signal) in the
to the limited FoV in MRI, especially for patients acquired PET images, as opposed to metal artifacts in PET/CT. In [52],
with the arms down (Fig. 6). Increasing the MR bore diameter Hofmann et al. showed that in 2 out of 3 patients with metal
would eliminate this limitation but would be extremely costly. implants a template-based approach could partly alleviate the
If the MR-based attenuation map is truncated, it can have an problem. Yet, as long as no robust method able to account
important effect on the attenuation correction, especially for for metal artifacts is available in commercial scanners, the
regions near the arms. Furthermore, implementations of the image readers should be aware of this limitation and carefully
scatter correction which sample the outside part of the patient analyze the regions surrounding metal implants.
assuming that all events detected outside are scattered events
[25] might result in a severely biased scatter scaling factor in
the presence of truncation. A simple method to account for Determination of the hardware attenuation
that estimating the patient contour based on the uncorrected map
PET images has been reported [65,66]; however, the approach
needs tracer uptake in the truncated regions and tends to create The photon attenuation and scatter within the FoV happens
a convex hull out of the body contour, unable to delineate the not only with the patient’s body but also with the hardware
gap between the arms and the chest. To overcome these limi- present between the patient and the PET detectors. This is
tations, a simultaneous emission-transmission reconstruction particularly relevant in PET/MR imaging, where not only the
using the segmented MR-based attenuation map as starting patient bed is present in the FoV, but typically also coils
point has shown promising results [62,63]. More recently, to improve the MR signal and occasionally other compo-
a technique to enlarge the MR FoV by optimizing the gra- nents (positioning aids, patient monitoring devices, cables,
dient readout and using distortion correction has also been earphones, etc.). These hardware components are invisible in
investigated [67,68]. conventional MR sequences and thus will be absent in the
MR-based attenuation map.
A first important point is whether the attenuation produced
by the components is relevant enough to have an impact on the
data. Indeed, some components such as patient bed and head
coil have a clear impact on the attenuation, while for others
the effect is smaller.
The solution consists in precalculating attenuation models
of the hardware components and adding them at the correct
spatial location within the attenuation map (Fig. 7). Although
the idea is rather basic, its implementation is not. On one hand,
it is challenging to obtain accurate attenuation models because
CT-derived attenuation factors can in general not be easily
translated to 511 keV for non-human tissues; radionuclide
transmission imaging overcomes this problem at the expense
of a limited spatial resolution. On the other hand, the location
should be precisely known (within 1-2 mm) in order to avoid
having local errors above 5% [34,69,70].
The location can be reasonably well-known for rigid and
fixed components such as the patient bed as well as, when
applicable, head and spine coils attached to it. Other flexible
or movable components (e.g. most surface coils, positioning
aids and patient monitoring devices) cannot be currently taken
into account by this method [71–73]. Instead, they should be
redesigned to minimize their impact on the PET data by adapt-
ing the choice of the materials used and its spatial distribution.
Figure 6. Three-dimensional visualization of a stack of transaxial In fact, redesigning the components to minimize the attenua-
MR images acquired in overlapping packages. This demonstrates the tion is also convenient for components which can be corrected
impact of the limited FoV in xy-direction which causes truncation in with a precalculated attenuation model in order to preserve the
the arms and occasionally in the hips, breast or abdomen. PET image quality. However, this might require a complete
A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310 307

Figure 7. Transmission measurement of an MR head and neck coil acquired using a rotating Germanium source, reproduced from Delso
et al. [70] with permission from IOP Publishing Ltd. (a) Rendering of the head coil. (b) Axial, (c) sagittal and (d) coronal views of the
transmission scan of the head and neck coils.

re-design of currently available and highly sophisticated MR and whole-body imaging. For brain imaging, identification of
coils. bone is important due to the impact of the skull; segmentation-
based approaches using ultrashort echo time [33,34] and
template-based approaches [48–52] have both proven to be
Perspectives for attenuation and scatter successful at this task.
correction in PET/MR For whole-body imaging, a combination of several
approaches seems necessary. The segmentation approach has
The determination of the attenuation map in PET/MR imag- been reported to provide good results for separate PET/CT
ing is challenging. The same way PET and MR provide and MRI acquisitions [37,39,40] as well as for integrated
complementary information about the patient, the investigated PET/MR acquisitions in cardiology [74] and oncology [75].
approaches for attenuation correction are not necessarily alter- The approach has however three inherent limitations: under-
natives but also complement each other. As can be seen in estimation of tracer uptake for bone lesions; underestimation
Table 1, the best results can be achieved by combining differ- in the presence of metal; and errors due to the truncation of
ent approaches. the MR-based attenuation map, especially when the patient is
Regarding the hardware attenuation, precalculated attenu- acquired with the arms down. For the latter issue, the transax-
ation maps for the most attenuating components have to be ial FoV of the MR sequences used for whole-body AC should
included [34,69–72]. This approach is thus complementary to be maximized [67,68]; if this is not sufficient, the missing
any approach used for the patient attenuation. attenuation data should be recovered with a simultaneous
Concerning the photon attenuation produced by the patient, emission-transmission reconstruction of the region outside
different approaches appear to be necessary for brain imaging the FoV [62–64], profiting from time-of-flight PET data if
308 A. Martinez-Möller, S.G. Nekolla / Z. Med. Phys. 22 (2012) 299–310

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