Functional connectivity analysis of resting-state fMRI data has recently become one of the most common approaches to characterizing individual brain function. It has been widely suggested that the functional connectivity matrix is a useful approximate representation of the brain's connectivity, potentially providing behaviorally or clinically relevant markers. However, functional connectivity estimates are known to be detrimentally affected by various artifacts, including those due to in-scanner head motion. Moreover, as individual functional connections generally covary only very weakly with head motion estimates, motion influence is difficult to quantify robustly, and prone to be neglected in practice. Although the use of individual estimates of head motion, or group-level correlation of motion and functional connectivity has been suggested, a sufficiently sensitive measure of individual functional connectivity quality has not yet been established. We propose a new intuitive summary index, Typicality of Functional Connectivity, to capture deviations from standard brain functional connectivity patterns. In a resting-state fMRI dataset of 245 healthy subjects, this measure was significantly correlated with individual head motion metrics. The results were further robustly reproduced across atlas granularity, preprocessing options, and other datasets, including 1,081 subjects from the Human Connectome Project. In principle, Typicality of Functional Connectivity should be sensitive also to other types of artifacts, processing errors, and possibly also brain pathology, allowing extensive use in data quality screening and quantification in functional connectivity studies as well as methodological investigations.
- MeSH
- Artifacts MeSH
- Atlases as Topic * MeSH
- Datasets as Topic * MeSH
- Adult MeSH
- Head Movements MeSH
- Connectome * methods standards MeSH
- Humans MeSH
- Magnetic Resonance Imaging * methods standards MeSH
- Young Adult MeSH
- Brain diagnostic imaging physiology MeSH
- Image Processing, Computer-Assisted * methods standards MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Young Adult MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
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
- Algorithms * MeSH
- Electronic Data Processing statistics & numerical data MeSH
- Humans MeSH
- Magnetic Resonance Spectroscopy methods MeSH
- Magnetic Resonance Imaging methods MeSH
- Image Processing, Computer-Assisted methods MeSH
- Software * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
We argue that statistical practice in the social and behavioural sciences benefits from transparency, a fair acknowledgement of uncertainty and openness to alternative interpretations. Here, to promote such a practice, we recommend seven concrete statistical procedures: (1) visualizing data; (2) quantifying inferential uncertainty; (3) assessing data preprocessing choices; (4) reporting multiple models; (5) involving multiple analysts; (6) interpreting results modestly; and (7) sharing data and code. We discuss their benefits and limitations, and provide guidelines for adoption. Each of the seven procedures finds inspiration in Merton's ethos of science as reflected in the norms of communalism, universalism, disinterestedness and organized scepticism. We believe that these ethical considerations-as well as their statistical consequences-establish common ground among data analysts, despite continuing disagreements about the foundations of statistical inference.
- MeSH
- Data Interpretation, Statistical MeSH
- Humans MeSH
- Uncertainty MeSH
- Information Dissemination MeSH
- Models, Statistical MeSH
- Statistics as Topic * methods standards MeSH
- Research Design standards MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
