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BACKGROUND: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. RESULTS: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. CONCLUSIONS: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.
BACKGROUND: Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies, mostly performed on a single scanner model or data format, as there is no flexible way of documenting and exchanging processed magnetic resonance spectroscopy data in digital format. This is because the DICOM standard for spectroscopy deals with unprocessed data. This paper proposes a plugin tool developed for jMRUI, namely jMRUI2XML, to tackle the latter limitation. jMRUI is a software tool for magnetic resonance spectroscopy data processing that is widely used in the magnetic resonance spectroscopy community and has evolved into a plugin platform allowing for implementation of novel features. RESULTS: jMRUI2XML is a Java solution that facilitates common preprocessing of magnetic resonance spectroscopy data across multiple scanners. Its main characteristics are: 1) it automates magnetic resonance spectroscopy preprocessing, and 2) it can be a platform for outputting exchangeable magnetic resonance spectroscopy data. The plugin works with any kind of data that can be opened by jMRUI and outputs in extensible markup language format. Data processing templates can be generated and saved for later use. The output format opens the way for easy data sharing- due to the documentation of the preprocessing parameters and the intrinsic anonymization--for example for performing pattern recognition analysis on multicentre/multi-manufacturer magnetic resonance spectroscopy data. CONCLUSIONS: jMRUI2XML provides a self-contained and self-descriptive format accounting for the most relevant information needed for exchanging magnetic resonance spectroscopy data in digital form, as well as for automating its processing. This allows for tracking the procedures the data has undergone, which makes the proposed tool especially useful when performing pattern recognition analysis. Moreover, this work constitutes a first proposal for a minimum amount of information that should accompany any magnetic resonance processed spectrum, towards the goal of achieving better transferability of magnetic resonance spectroscopy studies.
- MeSH
- algoritmy * MeSH
- automatizované zpracování dat statistika a číselné údaje MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie metody MeSH
- magnetická rezonanční tomografie metody MeSH
- počítačové zpracování obrazu metody MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Magnetic resonance spectroscopic imaging (MRSI) involves a huge number of spectra to be processed and analyzed. Several tools enabling MRSI data processing have been developed and widely used. However, the processing programs primarily focus on sophisticated spectra processing and offer limited support for the analysis of the calculated spectroscopic maps. In this paper the jSIPRO (java Spectroscopic Imaging PROcessing) program is presented, which is a java-based graphical interface enabling post-processing, viewing, analysis and result reporting of MRSI data. Interactive graphical processing as well as protocol controlled batch processing are available in jSIPRO. jSIPRO does not contain a built-in fitting program. Instead, it makes use of fitting programs from third parties and manages the data flows. Currently, automatic spectra processing using LCModel, TARQUIN and jMRUI programs are supported. Concentration and error values, fitted spectra, metabolite images and various parametric maps can be viewed for each calculated dataset. Metabolite images can be exported in the DICOM format either for archiving purposes or for the use in neurosurgery navigation systems.
- MeSH
- automatizované zpracování dat statistika a číselné údaje MeSH
- Fourierova analýza MeSH
- funkční zobrazování neurálních procesů statistika a číselné údaje MeSH
- lidé MeSH
- magnetická rezonanční tomografie statistika a číselné údaje MeSH
- mozek metabolismus patologie MeSH
- programovací jazyk MeSH
- software * MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The myocardium examination by MR spectroscopy is very challenging due to movements caused by the cardiac rhythm and breathing. The aim of the study was to investigate the influence of breathing on the quantitative measurement of lipid/water ratios in different groups of volunteers and different measuring protocols. We examined the lipid content of myocardium at 3T using the proton single voxel spectroscopy. Three protocols (free breathing, breath hold and the use of respiratory navigator) controlled by ECG were used for the examination of 42 adult volunteers including 14 free divers. Spectra were evaluated using jMRUI software. An average content of lipids in the healthy interventricular septum, gained by all protocols was equal to 0.6 %, which is in agreement with other published data. Based on the quality of examinations and the highest technical success, the best protocol seems to be the one containing a respiratory navigator since it is more acceptable by patients. Based on our results and the literature data we can conclude that MR spectroscopy is able to distinguish patients from controls only if their myocardial lipid content is higher than 1.6 % (mean value of lipids plus two standard deviations).
- MeSH
- dospělí MeSH
- dýchání MeSH
- lidé MeSH
- lipidy analýza MeSH
- magnetická rezonanční spektroskopie metody MeSH
- metabolismus lipidů fyziologie MeSH
- mladiství MeSH
- mladý dospělý MeSH
- myokard metabolismus MeSH
- pilotní projekty MeSH
- plicní ventilace fyziologie MeSH
- protony MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
