2007 IEEE Nuclear Science Symposium Conference Record
A Simultaneous PET/MRI Scanner Based on RatCAP
in Small Animals
D. Schlyer, P.Vaska, D.Tomasi, C.Woody, S.-H. Maramraju, S.Southekal, J.-F.Pratte, S.Junnarkar, S.Solis-Najera,
S.Krishnamoorthy, A. Kriplani, S.Stoll
Abstract– The ability to acquire high resolution anatomical
data as well as quantitative functional information in vivo is
becoming an increasingly important factor in the diagnosis of
disease. Simultaneous acquisition of PET and MRI data would
provide essentially perfect co-registration between the two images
which is particularly important for tissues whose position and
shape can change between sequential scans. RatCAP is a complete
3D tomograph that is designed to image the brain of an awake
rat. A special MRI coil composed of 2 saddle elements working in
quadrature mode was mounted on a Delrin cylinder specifically
designed to fit inside the RatCAP but allowing the rat’s head to
be placed inside as well. Simultaneous PET/MRI images of the rat
brain have been acquired in a 4T MRI scanner using the RatCAP
detector, with minimal effect on MRI images.
I. INTRODUCTION
T HE ability to combine two different imaging modalities
that complement each other in obtaining high resolution
anatomical and quantitative functional information can be
of great value for in vivo imaging studies. Positron Emission
Tomography (PET) combined with X-ray Computed
Tomography (CT) has proved to be a very valuable imaging
tool for diagnosing tumors [1]-[3]. Good anatomical detail
obtained from CT can be fused with physiological information
of the body obtained from PET. However, this sequential
procedure may lead to imperfect co-registration of the images
due to the change of position and shape of tissue between
scans [4]. Also, CT comes with additional radiation dose and
does not provide good soft tissue contrast. Magnetic resonance
imaging (MRI) provides good or better anatomical detail.
Simultaneous PET/MRI imaging in small animals has been of
great interest for studying the neuroreceptor interactions, drug
distributions, tumor cell metabolism, and neuroreceptor brain
mapping. Better delineation of tissue boundaries and
correction for partial volume effects is possible in PET images
for small regions or organs of the body. Current imaging
research groups are focusing on combining PET and MRI
imaging to obtain simultaneous images from both modalities
[5]-[9].
Manuscript received November 23, 2007. This research was carried out at
Brookhaven National Laboratory under contract DE-AC02-98CH10886 with
the U.S. Department of Energy as collaboration between BNL and the State
University of New York at Stony Brook.
Most authors are with Brookhaven National Laboratory, Upton, NY (e-
mail: schlyer@bnl.gov, telephone: 631-344-4587).
S.-H. Maramraju, S. Southekal, S. Krishnamoorthy and A. Kriplani are
with Biomedical Engineering department, State University of New York at
Stony Brook, Stony Brook, NY.
.
1-4244-0923-3/07/$25.00 ©2007 IEEE.
M16-3
One of the main challenges for developing a PET/MRI
scanner has been the effect of the high MRI magnetic fields on
photomultiplier tubes (PMTs) and the tendency of the
magnetic fields to interfere with the PET readout electronics
[10]. The magnetic components in PET can cause
inhomogeneities in the field leading to susceptibility artifacts
in the MRI images. In contrast to photomultiplier tubes,
avalanche photodiodes (APDs) show great promise in the
design of PET scanners that can operate in high magnetic
fields [9], [11]. An MRI compatible PET scanner based on Rat
Conscious Animal PET (RatCAP) has been developed for
simultaneous acquisition of MRI and PET images. Our
approach utilizes block detectors consisting of pixelated arrays
of LSO crystals, read out with matching arrays of avalanche
photodiodes (APDs) and a custom-designed Application
Specific Integrated Circuit (ASIC) [12]. Our goal is to
construct a PET detector that will not interfere with the MRI
image acquisition, can withstand pulsed (radio-frequency) RF
power, and can function in the presence of high magnetic
fields.
II. METHODS
A. New RatCAP Design:
The RatCAP is a 3D ring tomograph (Fig. 1(a)) that is
comprised of 12 block detectors, each of which consists of a 4
x 8 array of 2.2 x 2.2 x 5 mm3 LSO crystals read out with a
matching APD array (Hamamatsu S8550) [13]. To improve
the performance of the detector, many modifications have been
made to the front-end ASIC (Fig. 1(c)) leading to a measured
Equivalent Noise Charge (ENC) of ~ 650 electrons rms, a
factor of ~2 improvement over the ENC achieved by the
original design [12], [14]. The Charge Sensitive Preamplifier
(CSP) was completely redesigned. Gain programmability has
been implemented in this version with a gain ratio from 1 to
2.72 divided in 31 steps. All the digital I/Os from single ended
1.8V CMOS were replaced with Low Voltage Differential
Signaling (LVDS), leading to a significant noise reduction on
the non-magnetic rigid flex Printed Circuit Board (PCB)
readout, (shown in Fig. 1(b)). The LVDS receiver has a power
consumption of 3.3 mW and the LVDS transmitter of 15.9
mW. Other features include dual-energy window mode and
programmable analog monitor for testing purposes.
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 b)

Rigid
LSO detectors
flex

(a) (b)

Fig.2. MRI coil array (right) inside the RatCAP (left).

Flex circuit board covered with

Copper case RatCAP
(c) ASICs (d)
Fig. 1. New RatCAP design. (a) RatCAP geometry. (b) RatCAP rigid flex
PCB with LSO detectors in a panel, later rolled into a detector ring (c) with
ASICs on the rear end. (d) TSPM board processes the ASIC signals.

Fig. 1(d) shows the Time to Digital Converter and Signal

Processing Module (TSPM), which receives and processes the Bedding for animal
detected signals from the RatCAP [15]. It consists of Field
Programmable Gate Array (FPGA) that timestamps the
asynchronous leading edge of each singles event. The
processed signals are then transmitted to a PCI based data Fig. 3. RatCAP support system is realized for systematic arrangement of
positioning the animal as well as supporting the RatCAP electronics.
acquisition and control PCB (PACRAT) via 2 Gigabit fiber
optic links. The firmware and software program upgrades were
made accordingly, for the new designs. This new version also C. RatCAP Image reconstruction:
has a larger aperture (40 mm) and can accommodate larger The data is processed in singles list mode and a coincidence
crystals (up to 7 mm) which will improve the sensitivity by a program reads 64-bit single events and identifies block and
factor of ~2. Almost all parts of the RatCAP are made of non- crystal IDs and timestamps. Prior to coincidence processing,
magnetic components and thoroughly shielded to minimize the events are sorted by their respective timestamps. Image
any electromagnetic interference. reconstruction is done using 3D Maximum likelihood
B. MRI Components: expectation maximization (MLEM) algorithm using an
accurate system matrix.
A special MRI RF coil made out of etched copper strip has
been designed where the coil is inserted in the RatCAP
detector (Fig. 2). The RF coil consists of two saddle elements III. PET/MRI INTERFERENCE
working in quadrature mode mounted on the Delrin ring. The
A. Effect of MRI on RatCAP
coil is tuned and matched at 170.29 MHz using the tuning
capacitors located six centimeters away from the RF array. The Background noise measurements were carried out without
coil is then inserted into the RatCAP. This coil is designed to any radioactive source and with the RF coil inserted in the
operate in close proximity of the RatCAP. RatCAP in the MRI scanner. The RatCAP shielding is coupled
A new non-magnetic support system was designed to to the Faraday cage of the MRI room. For the spin-echo
position the RatCAP in the MRI scanner during MRI scans, as sequences with TE/TR = 21/114 ms per slice, it was observed
shown in Fig. 3. This system supports the rigid flex of the that the number of singles had increased during the duration of
RatCAP and its electronics. This arrangement also allows RF pulsing (Fig. 4). This pattern of spikes of spurious singles
better positioning of the animal in the RatCAP. The rigid flex is seen in all the RF ON conditions. On the other hand, the
circuit from the RatCAP is wrapped with copper tape. The gradients had little effect on the RatCAP.
(tether) board is also covered with a copper lid and is wrapped
with an aluminum foil for better shielding from RF pulses.
The cables carrying the digital signals from the RatCAP to the
TSPM is shielded with non-magnetic braid. Rat brain images
were acquired in a 4 Tesla whole-body Varian/Siemens
system.

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 MRI

TE = 21 ms
900
1800

TR = 114 ms
PET

11 ms 11 ms

PET/MRI

(a)
Fig. 4. Number of Singles increased when RF pulses are turned ON.

PET/MRI
B. Effect of RatCAP on MRI
The effect of PET electronics on MRI was minimal and we
have obtained MRI images with the RatCAP in the MRI
scanner. However, since the head of the animal is in contact
with the RF coil, it led to some non-uniform sensitivity in the
MR image. The close proximity of aluminum housing of the
RatCAP to the RF coil resulted in excessive absorption of RF PET
power, leading to low MR signal-to-noise ratio (SNR). Also,
minimal image artifacts were noticeable due to the eddy
currents originating from the aluminum ring. Fig. 5 shows a
proton density image with spin echo sequence (TE/TR =
21/1700 ms) of a Sprague-Dawley rat weighing 250g MRI
administered with ~2 mCi of C-11 Methamphetamine.

(b)

MRI

Fig. 5. Proton density MRI image of the rat, with RatCAP detector electronics
in place.
PET
IV. IMAGE RESULTS
Phantom and rat brain images were acquired in a 4 Tesla
whole-body Varian/Siemens system. The images from these
scans are shown in Fig. 6. These images were obtained
simultaneously. PET/MRI
Fig. 6. PET/MRI co-registered images of (a) C-11 raclopride Striata phantom,
(b) F-18 FDG euthanized rat and (c) C-11 Methamphetamine administered
anesthetized rat image. For images shown in (a) and (c), the top row is the
MR image, the second row is the PET image and the third row is the co-
registered image. This order is flipped for image (b).
(c)

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 V. DISCUSSION
A new version of the RatCAP tomograph suited for PET/MRI
studies has been constructed with several improvements over
the previous version [13]. We have redesigned the ASIC, flex
circuit and data acquisition system to improve their
performance and make them more robust, both electronically
and mechanically. The ASIC has had several improvements
including built in ESD protection, programmable gain, dual
level discriminator for triggering allowing an energy window
to be set, lower noise which gives better timing resolution, and
the use of Low Voltage Differential Signaling (LVDS) which
decreases the chance of interference between the low level
analog signals from the APDs and the digital signals used for
data transmission.
The new version also has a larger aperture (40 mm) and can
accommodate larger crystals (up to 7 mm) for improved
sensitivity (~ x2). Care has been taken to improve the
shielding between the PET and MRI electronics in order to
minimize the eddy currents in the aluminum ring. From the
background noise measurements, it is clear that the RF pulses
have a greater effect on the PET electronics than the gradients.
However, a threshold can be set to eliminate the spurious noise
counts from the data. Also, since the repetition time of RF
pulses is known, the data resulting from RF pulses can be
discarded by gating the RF pulses while acquiring PET data.
Based on analysis of the current data, the gating results in a
loss of only 7 % of the acquired data, but we believe that we
can improve that efficiency with better shielding.
From the animal scans, we have obtained better
simultaneous PET/MR images than before [16]. However, low
SNR and image artifacts due to eddy currents in the aluminum
ring are visible in the MR images. A segmented G-10 copper
case shielding with a copper coated thickness of 5 μm has
been constructed. We are planning to house the RatCAP
detector electronics in this gridded copper case to minimize
the effect of eddy currents in higher magnetic fields. Work is
underway to use RatCAP in a Bruker 9.4T small animal MRI
scanner and to further develop PET compatible RF coils with
improved SNR.
VI. CONCLUSION
We have demonstrated that the PET detector works inside the
MRI field using 511 keV gamma rays, and have obtained MRI
images with various detector components that show minimal
distortion in the MRI image. An upgraded version of the
RatCAP PET tomograph has been designed and fabricated
with all the ASIC improvements, better shielding and all non-
magnetic components and it has provided better simultaneous
PET/MRI images. In future, we would like to develop a whole
body mouse scanner compatible with the 9.4T microMRI
scanner and also explore other medical applications such as a
simultaneous PET/MRI breast scanner.
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ACKNOWLEDGMENT
The authors would like to thank Daniela Schulz and Vinal
Patel for providing and handling animals in this study, David
Alexoff for assistance in radiotracer administration in animals
and Ruiliang Wang for technical assistance in running MRI
sequences. This work was supported by the U.S. Department
of Energy (OBER) under Prime Contract No. DE-AC02-
98CH10886.
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