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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 committee. 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 models. 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: -
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 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