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  An open source triggered CEST module for Bruker systems for reliable CEST MRI with efficient motion artifact mitigation

Mueller, S., Pohmann, R., Chiaffarelli, R., Hoffmann, S., Martins, A., Scheffler, K., et al. (2021). An open source triggered CEST module for Bruker systems for reliable CEST MRI with efficient motion artifact mitigation. Magnetic Resonance Materials in Physics, Biology and Medicine, 34(Supplement 1): S3.O1, S18-S19.

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Mueller, S1, 2, Author           
Pohmann, R1, 2, Author           
Chiaffarelli, R, Author
Hoffmann, SHL, Author
Martins, AF, Author
Scheffler, K1, 2, Author           
Zaiss, M1, 2, Author           
1Department High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497796              
2Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497794              


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 Abstract: Introduction: Chemical exchange saturation transfer (CEST) MRI is
an outstanding tool to investigate biological questions. However,
motion artifacts are a major problem as CEST experiments are performed
over several minutes. This issue was highlighted for CEST
MRI in humans1 but lacks attention in animal studies. Moreover,
many animal experiments employ xenografts in the abdomen, where
motion is even more severe and rigid body motion correction is not
feasible. We demonstrate such artifacts exemplarily and propose to
mitigate motion artifacts using a module that includes triggered
acquisition after reaching and keeping a CEST steady-state (SS)
saturation. This enables reliable snapshot2 CEST MRI triggered to
breathing cycle of the animal and is provided as open source library.
Methods: The idea is to perform CEST MRI in a snapshot like
manner in SS. Instead of a continuous wave (CW) preparation of fixed
duration, quasi-CW allows to extend the duration of the preparation as
long as necessary to reach a certain phase within the breathing cycle
(Fig. 1A). Both quasi-CW and CW preparation yield consistent
results (Fig. 1BC). Frequency offsets for CEST preparation are read
from a text file or are equally spaced within a certain range. Parameters
such as pulse duration, inter-pulse delay, B1 and recovery times
are adjusted via the extended graphical user interface. The CEST
module is contained in source code files, which are independent of the
image readout’s (RO) source code. They get included into the existing
RO by a simple #include command. Additionally, some minor
modifications need to be done manually to ensure full functionality of
the RO. A template that shows how to modify the existing RO
accordingly is provided. All source code is available via gitlab.com/
SebMue/cest_module_for_bruker. The proposed CEST module was
used with Bruker’s FISP RO in an egg white phantom and in the
abdomen of a healthy rat. Experiments were performed on Bruker’s
14.1 T (phantom) and 7 T BioSpec systems (animal). Animal
experiments were performed in accordance with the local ethics
Discussion: It was demonstrated, how severe motion artifacts bias
CEST MRI in animals. With the proposed open source module, this
issue was significantly reduced. The modular source code requires
only minimal manual programming to include it into an existing RO.
We hope the proposed open source module is useful for other research
groups, and will facilitate improved CEST experiments in animal
A healthy experienced volunteer was scanned on a 7 T MR system
(MAGNETOM Terra, Siemens Healthineers, Erlangen, Germany)
using a multi-echo 3D gradient echo sequence (RF- and gradientspoiled)
at an isotropic resolution of 0.8 mm (TR 25 ms, 8 equally
spaced echoes TE 2.8.. 18.9 ms, FA 8 and 25 degrees). The image
pairs for T1 mapping with variable flip angles were acquired three
times with different on-resonance excitation pulses of sinc window
shape and lengths: (a) equal (both 560 ls)3, (b) scaled linearly for
constant B1
peak (180, 560 ls)4 and (c) scaled quadratically for
constant B1
RMS (140, 1368 ls)2. B1
? was mapped by the SE/STE
EPI method5.
Quantitative maps were calculated with the hMRI-toolbox6 within the
SPM12 framework (https://www.fil.ion.ucl.ac.uk/spm/software/
spm12/) in MATLAB (Mathworks, Natick, USA). The same toolbox
was used to compute maps of tissue probability.
Results: Simulations (Fig. 1) demonstrate the expected variations in
bound-pool saturation and steady-state signal in the three regimes
(equal pulse lengths, constant B1
peak, constant B1
RMS). In vivo
results (Fig. 2) reveal that constant B1
RMS scaling leads to tighter
clustering of grey and white matter T1 values, suggesting lower
spatial bias. An example slice shown in Fig. 3 also shows lower
spatial bias and a sharper white matter/grey matter interface.


 Dates: 2021-09
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1007/s10334-021-00947-8
 Degree: -


Title: 38th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB 2021)
Place of Event: -
Start-/End Date: 2021-10-07 - 2021-10-09

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Title: Magnetic Resonance Materials in Physics, Biology and Medicine
Source Genre: Journal
Publ. Info: Amsterdam : No longer published by Elsevier
Pages: - Volume / Issue: 34 (Supplement 1) Sequence Number: S3.O1 Start / End Page: S18 - S19 Identifier: ISSN: 0968-5243
CoNE: https://pure.mpg.de/cone/journals/resource/954926245532