Preclinical ORYX-MRS: Toolbox for Proton Magnetic Resonance Spectroscopy Data Analysis in Rat Brain
Poster No:
1567
Submission Type:
Abstract Submission
Authors:
Melisa Özakçakaya1, Sevim Cengiz2, Arnold Benjamin3, Uluç Pamuk1, Oğuzhan Hüraydın1, Pınar Özbay1, Ruslan Garipov3, Esin Öztürk Işık1
Institutions:
1Boğaziçi University, Istanbul, Istanbul, 2Zayed University, Abu Dhabi, Abu Dhabi, 3MR Solutions Ltd, Guildford, Guildford
First Author:
Co-Author(s):
Introduction:
Proton magnetic resonance spectroscopy (¹H-MRS) is a non-invasive imaging technique that could provide metabolic information of the brain. A short echo time of ¹H-MRS can detect more than fifteen different metabolites (Bogner et al., 2017, Mahmoudi et al., 2023). Rodent models are widely used in preclinical studies due to their genetic similarity to humans, ease of genetic manipulation, and well-established protocols for modeling human diseases. Preclinical studies using ¹H-MRS could help with understanding the underlying mechanism of brain disease processes, monitoring disease progression, and treatment planning (Lanz et al., 2020). While several clinical MR spectroscopy tools (Clarke et al., 2020, Oeltzschner et al., 2020) have advanced capabilities for MR spectral data analysis and visualization, they are designed for human studies and are less effective for preclinical research. Oryx-MRSI is a versatile tool designed for ¹H-MRSI analysis, offering features such as data visualization, image registration, and atlas-based statistical analysis for clinical MRI scanner data (Cengiz et al., 2022). This study aims to bridge the gap in preclinical ¹H-MRS data analysis by introducing a toolbox dedicated to preclinical studies within ORYX-MRSI, especially designed for rat brain ¹H-MRS analysis, with a user-friendly graphical user interface called 'Preclinical Oryx-MRS'.
Methods:
Preclinical ORYX-MRS was programmed in MATLAB 2024a (The Mathworks Inc., Natick, MA). The software currently accepts various data input files from the user, including a raw ¹H-MRS data file in .mrd format, LCModel output .coord file, and reference anatomical MRI. The toolbox currently has three main modules, which are load data, co-registration, and registration.
Load Data
This module reads the raw ¹H-MRS data that was acquired as a .mrd file or an LCModel output .coord file, and it can visualize the data. The user can switch between the raw data and .coord file visualizations.
Co-registration
In this module, a volume of interest (VOI) mask is created based on the offset, angle, and size information that comes from the .mrd file and the created mask is co-registered onto the NIfTI formatted anatomical reference MRI. The mask file generated is then saved as a NIfTI file, and SPM12 software is used to visualize the reference MRI and overlaid VOI mask.
Registration
This module registers the anatomical reference MRI onto the SIGMA rat brain atlas (Liu et al., 2019). For this task, FMRIB's Linear Image Registration Tool (FSL FLIRT) (Jenkinson & Smith, 2001) is used. After the registration of the reference MRI onto the atlas, the obtained transformation matrix is then used to register the binary VOI mask onto the atlas. The registered anatomical MRI and the mask file are then saved in NIfTI format.
Toolbox Assessment
To assess the toolbox, a .coord file from an open-source study (Simicic et al., 2021), and an .mrd file and a reference T2-weighted anatomical MRI (TR/TE=5000/45 ms, slice thickness= 1 mm) acquired using a 7T preclinical MR scanner (MR Solutions, Guildford, UK) were utilized.
Load Data
This module reads the raw ¹H-MRS data that was acquired as a .mrd file or an LCModel output .coord file, and it can visualize the data. The user can switch between the raw data and .coord file visualizations.
Co-registration
In this module, a volume of interest (VOI) mask is created based on the offset, angle, and size information that comes from the .mrd file and the created mask is co-registered onto the NIfTI formatted anatomical reference MRI. The mask file generated is then saved as a NIfTI file, and SPM12 software is used to visualize the reference MRI and overlaid VOI mask.
Registration
This module registers the anatomical reference MRI onto the SIGMA rat brain atlas (Liu et al., 2019). For this task, FMRIB's Linear Image Registration Tool (FSL FLIRT) (Jenkinson & Smith, 2001) is used. After the registration of the reference MRI onto the atlas, the obtained transformation matrix is then used to register the binary VOI mask onto the atlas. The registered anatomical MRI and the mask file are then saved in NIfTI format.
Toolbox Assessment
To assess the toolbox, a .coord file from an open-source study (Simicic et al., 2021), and an .mrd file and a reference T2-weighted anatomical MRI (TR/TE=5000/45 ms, slice thickness= 1 mm) acquired using a 7T preclinical MR scanner (MR Solutions, Guildford, UK) were utilized.
Results:
Figure 1 shows the interface of the toolbox with the current three modules. Additionally, visualizations of a raw ¹H-MRS data file and a .coord file can be seen in this figure. Figure 2 displays a VOI mask co-registered onto a T2-weighted MRI of a rat brain, and registration of the T2w MRI onto the SIGMA atlas.
·Figure 1. Load Data module for visualizing A) the raw ¹H-MRS data, and B) the .coord file
·Figure 2. The coregistration module (A) and the registration module (B)
Conclusions:
Preclinical- ORYX MRS is a user-friendly ¹H-MRS data analysis software created as a part of the ORYX-MRSI tool. This toolbox includes three modules so far to read and visualize the MR spectral data, to create a VOI mask and co-register it to the reference anatomical MRI, and to register both anatomical MRI and the VOI mask to the SIGMA atlas. Future studies will add the LCmodel quantification of the .mrd file and the statistical data analysis module to the toolbox.
Acknowledgments
This study is funded by TUBITAK 1004 grant (22AG016).
Acknowledgments
This study is funded by TUBITAK 1004 grant (22AG016).
Modeling and Analysis Methods:
Methods Development 1
Novel Imaging Acquisition Methods:
MR Spectroscopy 2
Keywords:
ANIMAL STUDIES
Data analysis
Magnetic Resonance Spectroscopy (MRS)
Open-Source Software
1|2Indicates the priority used for review
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9. Simicic, D. (2021). In vivo macromolecule signals in rat brain 1H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T2 relaxation times. Magnetic Resonance in Medicine, 86(5), 2384–2401.