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Purpose: Medulloblastoma is the most common malignant brain tumor occurring in childhood and is a significant cause of morbidity and mortality in pediatric oncology. More intense treatment strategies are recommended for patients displaying high-risk factors; however, considerable variation in outcome remains, indicating a need for improved predictive markers. In this study, 1H magnetic resonance spectroscopy (MRS) was used to investigate noninvasive molecular biomarkers of survival in medulloblastoma.Experimental Design: MRS was performed on a series of 35 biopsy-confirmed medulloblastoma cases. One case was excluded because of poor quality MRS. The prognostic value of MRS detectable biomarkers was investigated using Cox regression, retrospectively (N = 15). A subsequent validation analysis (N = 19) was also performed to reduce the chance of type I errors. Where available, high-resolution ex vivo MRS of biopsy tissue was used to confirm biomarker assignments.Results: The retrospective analysis revealed that creatine, glutamate, and glycine were markers of survival (P < 0.01). The validation analysis showed that glutamate was a robust marker, with a hazard ration (HR) of 8.0 for the full dataset (P = 0.0003, N = 34). A good correlation between in vivo and ex vivo MRS glutamate/total-choline was found (P = 0.001), validating the in vivo assignment. Ex vivo glutamate/total-choline was also associated with survival (P < 0.01).Conclusion: The identification of glutamate as a predictive biomarker of survival in pediatric medulloblastoma provides a clinically viable risk factor and highlights the importance of more detailed studies into the metabolism of this disease. Noninvasive biomarker detection using MRS may offer improved disease monitoring and potential for widespread use following multicenter validation. Clin Cancer Res; 20(17); 4532–9. ©2014 AACR.

Supplementary Methods (Text 1). A description of the treatment protocols used during the study period. Supplementary Figure 1. Example medulloblastoma fits where the lowest smooth black line is the baseline; the middle black line represents the acquired spectrum following pre-processing; the red line shows the spectral fit and the top black line shows the residual between the fit and acquired spectrum. A) shows a distorted baseline leading to qc failure whereas B) is an example of an ideal smooth baseline.

Despite many differences, autism spectrum disorder and schizophrenia spectrum disorder share environmental risk factors, genetic predispositions as well as neuronal abnormalities, and show similar cognitive deficits in working memory, perspective taking, or response inhibition. These alterations are already present in subclinical traits of these disorders. The literature proposes that alterations in the inhibitory GABAergic and the excitatory glutamatergic system could explain underlying neuronal commonalities and differences. Using magnetic resonance spectroscopy (1H-MRS), we investigated the associations between glutamate concentrations in the anterior cingulate cortex (ACC), the left/right putamen, and left/right dorsolateral prefrontal cortex and psychotic-like experiences (schizotypal personality questionnaire) and autistic traits (autism spectrum quotient) in 53 healthy individuals (28 women). To investigate the contributions of glutamate concentrations in different cortical and subcortical regions to symptom expression and their interactions, we used linear regression and moderation analyses. We found that glutamate concentration in the ACC but in none of the other regions predicted positive-like symptoms. None of the other clinical scores was associated with altered levels of glutamate. Specifying this finding, the moderation analysis showed that increased ACC glutamate was predictive of positive-like symptoms when glutamate concentrations in the right putamen were reduced, and that increased ACC glutamate was predictive of positive-like symptoms when disorganized traits were attenuated. This study provides evidence that an imbalance in the glutamatergic neurotransmitter system involving cortical and subcortical regions is linked to the expression of psychotic-like experiences, especially positive-like symptoms. These findings may facilitate the detection of individuals transitioning into an acute episode of psychosis.

Purpose Accurate baseline modeling is essential for reliable MRS analysis and interpretation-particularly at short echo-times, where enhanced metabolite information coincides with elevated baseline interference. The degree of baseline smoothness is a key analysis parameter for metabolite estimation, and in this study, a new method is presented to estimate its optimal value. Methods An adaptive baseline fitting algorithm (ABfit) is described, incorporating a spline basis into a frequency-domain analysis model, with a penalty parameter to enforce baseline smoothness. A series of candidate analyses are performed over a range of smoothness penalties, as part of a 4-stage algorithm, and the Akaike information criterion is used to estimate the appropriate penalty. ABfit is applied to a set of simulated spectra with differing baseline features and experimentally acquired 2D MRSI-both at a field strength of 3 Tesla. Results Simulated analyses demonstrate metabolite errors result from 2 main sources: bias from an inflexible baseline (underfitting) and increased variance from an overly flexible baseline (overfitting). In the case of an ideal flat baseline, ABfit is shown to correctly estimate a highly rigid baseline, and for more realistic spectra a reasonable compromise between bias and variance is found. Analysis of experimentally acquired data demonstrates good agreement with known correlations between metabolite ratios and the contributing volumes of gray and white matter tissue. Conclusions ABfit has been shown to perform accurate baseline estimation and is suitable for fully automated routine MRS analysis.

Edited MRS sequences are widely used for studying γ-aminobutyric acid (GABA) in the human brain. Several algorithms are available for modelling these data, deriving metabolite concentration estimates through peak fitting or a linear combination of basis spectra. The present study compares seven such algorithms, using data obtained in a large multisite study. GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate. After referencing metabolite estimates (to water or creatine), systematic differences in scale were observed between datasets acquired on different vendors' hardware, presenting across algorithms. Scale differences across algorithms were also observed. Using the correlation between metabolite estimates and voxel tissue fraction as a benchmark, most algorithms were found to be similarly effective in detecting differences in GABA+. An interclass correlation across all algorithms showed single-rater consistency for GABA+ estimates of around 0.38, indicating moderate agreement. Upon inclusion of a basis set component explicitly modelling the macromolecule signal underlying the observed 3.0 ppm GABA peaks, single-rater consistency improved to 0.44. Correlation between discrete pairs of algorithms varied, and was concerningly weak in some cases. Our findings highlight the need for consensus on appropriate modelling parameters across different algorithms, and for detailed reporting of the parameters adopted in individual studies to ensure reproducibility and meaningful comparison of outcomes between different studies. publishedVersion

Our understanding of how information unfolds when we recall events from memory remains limited. In this study, we investigate whether the reconstruction of visual object memories follows a backward trajectory along the ventral visual stream with respect to perception, such that their neural feature representations are gradually reinstated from late areas close to the hippocampus backwards to lower-level sensory areas. We use multivariate analyses of fMRI activation patterns to map the constituent features of the object memories onto the brain during retrieval, and EEG-fMRI fusion to track the temporal evolution of the reactivated patterns. Participants studied new associations between verbs and randomly paired object images in an encoding phase, and subsequently recalled the objects when presented with the corresponding verb cue. Decoding reactivated memory features from fMRI activity revealed that retrieval patterns were dominated by conceptual features, represented in comparatively late visual and parietal areas. Representational-similarity-based fusion then allowed us to map the EEG patterns that emerged at each given time point of a trial onto the spatially resolved fMRI patterns. This fusion suggests that memory reconstruction proceeds backwards along the ventral visual stream from anterior fronto-temporal to posterior occipital and parietal regions, in line with a semantic-to-perceptual gradient. A linear regression on the peak time points of reactivated brain regions statistically confirms that the temporal progression is reversed with respect to encoding. Together, the results shed light onto the spatio-temporal trajectories along which memories are reconstructed during associative retrieval, and which features of an image are reconstructed when in time and where in the brain.

IntroductionEvidence suggests a potentially causal role of interleukin 6 (IL-6), a pleiotropic cytokine that generally promotes inflammation, in the pathogenesis of psychosis. However, no interventional studies in patients with psychosis, stratified using inflammatory markers, have been conducted to assess the therapeutic potential of targeting IL-6 in psychosis and to elucidate potential mechanism of effect. Tocilizumab is a humanised monoclonal antibody targeting the IL-6 receptor to inhibit IL-6 signalling, licensed in the UK for treatment of rheumatoid arthritis. The primary objective of this study is to test whether IL-6 contributes to the pathogenesis of first episode psychosis and to examine potential mechanisms by which IL-6 affects psychotic symptoms. A secondary objective is to examine characteristics of inflammation-associated psychosis.Methods and analysisA proof-of-concept study employing a randomised, parallel-group, double-blind, placebo-controlled design testing the effect of IL-6 inhibition on anhedonia in patients with psychosis. Approximately 60 participants with a diagnosis of schizophrenia and related psychotic disorders (ICD-10 codes F20, F22, F25, F28, F29) with evidence of low-grade inflammation (IL-6≥0.7 pg/mL) will receive either one intravenous infusion of tocilizumab (4.0 mg/kg; max 800 mg) or normal saline. Psychiatric measures and blood samples will be collected at baseline, 7, 14 and 28 days post infusion. Cognitive and neuroimaging data will be collected at baseline and 14 days post infusion. In addition, approximately 30 patients with psychosis without evidence of inflammation (IL-6Ethics and disseminationThe study is sponsored by the University of Bristol and has been approved by the Cambridge East Research Ethics Committee (reference: 22/EE/0010; IRAS project ID: 301682). Study findings will be published in peer-review journals. Findings will also be disseminated by scientific presentation and other means.Trial registration numberISRCTN23256704.

Clinical coding uses a classification system to assign standard codes to clinical terms and so facilitates good clinical practice through audit, service design and research. However, despite clinical coding being mandatory for inpatient activity, this is often not so for outpatient services, where most neurological care is delivered. Recent reports by the UK National Neurosciences Advisory Group and NHS England’s ‘Getting It Right First Time’ initiative recommend implementing outpatient coding. The UK currently has no standardised system for outpatient neurology diagnostic coding. However, most new attendances at general neurology clinics appear to be classifiable with a limited number of diagnostic terms. We present the rationale for diagnostic coding and its benefits, and the need for clinical engagement to develop a system that is pragmatic, quick and easy to use. We outline a scheme developed in the UK that could be used elsewhere.

MRS can provide high accuracy in the diagnosis of childhood brain tumours when combined with machine learning. A feature selection method such as principal component analysis is commonly used to reduce the dimensionality of metabolite profiles prior to classification. However, an alternative approach of identifying the optimal set of metabolites has not been fully evaluated, possibly due to the challenges of defining this for a multi‐class problem. This study aims to investigate metabolite selection from in vivo MRS for childhood brain tumour classification. Multi‐site 1.5 T and 3 T cohorts of patients with a brain tumour and histological diagnosis of ependymoma, medulloblastoma and pilocytic astrocytoma were retrospectively evaluated. Dimensionality reduction was undertaken by selecting metabolite concentrations through multi‐class receiver operating characteristics and compared with principal component analysis. Classification accuracy was determined through leave‐one‐out and k‐fold cross‐validation. Metabolites identified as crucial in tumour classification include myo‐inositol (P < 0.05, AUC = 0 . 81 ± 0 . 01 ), total lipids and macromolecules at 0.9 ppm (P < 0.05, AUC = 0 . 78 ± 0 . 01 ) and total creatine (P < 0.05, AUC = 0 . 77 ± 0 . 01 ) for the 1.5 T cohort, and glycine (P < 0.05, AUC = 0 . 79 ± 0 . 01 ), total N‐acetylaspartate (P < 0.05, AUC = 0 . 79 ± 0 . 01 ) and total choline (P < 0.05, AUC = 0 . 75 ± 0 . 01 ) for the 3 T cohort. Compared with the principal components, the selected metabolites were able to provide significantly improved discrimination between the tumours through most classifiers (P < 0.05). The highest balanced classification accuracy determined through leave‐one‐out cross‐validation was 85% for 1.5 T 1H‐MRS through support vector machine and 75% for 3 T 1H‐MRS through linear discriminant analysis after oversampling the minority. The study suggests that a group of crucial metabolites helps to achieve better discrimination between childhood brain tumours.

Edited MRS sequences are widely used for studying GABA in the human brain. Several algorithms are available for modelling these data, deriving metabolite concentration estimates through peak fitting or a linear combination of basis spectra. The present study compares seven such algorithms, using data obtained in a large multi-site study.GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate.After referencing metabolite estimates (to water or creatine), systematic differences in scale were observed between datasets acquired on different vendors’ hardware, presenting across algorithms. Scale differences across algorithms were also observed.Using the correlation between metabolite estimates and voxel tissue fraction as a benchmark, most algorithms were found to be similarly effective in detecting differences in GABA+. An inter-class correlation across all algorithms showed single-rater consistency for GABA+ estimates of around 0.38, indicating moderate agreement. Upon inclusion of a basis set component explicitly modelling the macromolecule signal underlying the observed 3.0 ppm GABA peaks, single-rater consistency improved to 0.44. Correlation between discrete pairs of algorithms varied, and was concerningly weak in some cases.Our findings highlight the need for consensus on appropriate modelling parameters across different algorithms, and for detailed reporting of the parameters adopted in individual studies to ensure reproducibility and meaningful comparison of outcomes between different studies.HighlightsGABA-edited MRS data from 222 healthy adults across 20 research sites were analyzedData were modelled using seven different algorithms, yielding GABA+ and Glx estimatesModerate agreement was seen across all the tested algorithmsAdding a component to represent co-edited macromolecule signals improved concordanceBaseline modelling emerged as major factor differentiating outcomes

PurposeThe use of multiple data formats in the MRS community currently hinders data sharing and integration. NIfTI-MRS is proposed as a standard MR spectroscopy data format, which is implemented as an extension to the neuroimaging informatics technology initiative (NIfTI) format.Using this standardised format will facilitate data sharing, ease algorithm development, and encourage the integration of MRS analysis with other imaging modalities.MethodsA file format based on the NIfTI header extension framework was designed to incorporate essential spectroscopic metadata and additional encoding dimensions. A detailed description of the specification is provided. An open-source command-line conversion program is implemented to enable conversion of single-voxel and spectroscopic imaging data to NIfTI-MRS. To provide visualisation of data in NIfTI-MRS, a dedicated plugin is implemented for FSLeyes, the FSL image viewer.ResultsAlongside online documentation, ten example datasets are provided in the proposed format. In addition, minimal examples of NIfTI-MRS readers have been implemented. The conversion software, spec2nii, currently converts fourteen formats to NIfTI-MRS, including DICOM and vendor proprietary formats.ConclusionThe proposed format aims to solve the issue of multiple data formats being used in the MRS community. By providing a single conversion point, it aims to simplify the processing and analysis of MRS data, thereby lowering the barrier to use of MRS. Furthermore, it can serve as the basis for open data sharing, collaboration, and interoperability of analysis programs. It also opens possibility of greater standardisation and harmonisation. By aligning with the dominant format in neuroimaging, NIfTI-MRS enables the use of mature tools present in the imaging community, demonstrated in this work by using a dedicated imaging tool, FSLeyes, as a viewer.

Purpose Heating of gradient coils and passive shim components is a common cause of instability in the B0 field, especially when gradient intensive sequences are used. The aim of the study was to set a benchmark for typical drift encountered during MR spectroscopy (MRS) to assess the need for real-time field-frequency locking on MRI scanners by comparing field drift data from a large number of sites. Method A standardized protocol was developed for 80 participating sites using 99 3T MR scanners from 3 major vendors. Phantom water signals were acquired before and after an EPI sequence. The protocol consisted of: minimal preparatory imaging; a short pre-fMRI PRESS; a ten-minute fMRI acquisition; and a long post-fMRI PRESS acquisition. Both pre- and post-fMRI PRESS were non-water suppressed. Real-time frequency stabilization/adjustment was switched off when appropriate. Sixty scanners repeated the protocol for a second dataset. In addition, a three-hour post-fMRI MRS acquisition was performed at one site to observe change of gradient temperature and drift rate. Spectral analysis was performed using MATLAB. Frequency drift in pre-fMRI PRESS data were compared with the first 5:20 minutes and the full 30:00 minutes of data after fMRI. Median (interquartile range) drifts were measured and showed in violin plot. Paired t-tests were performed to compare frequency drift pre- and post-fMRI. A simulated in vivo spectrum was generated using FID-A to visualize the effect of the observed frequency drifts. The simulated spectrum was convolved with the frequency trace for the most extreme cases. Impacts of frequency drifts on NAA and GABA were also simulated as a function of linear drift. Data from the repeated protocol were compared with the corresponding first dataset using Pearson's and intraclass correlation coefficients (ICC). Results Of the data collected from 99 scanners, 4 were excluded due to various reasons. Thus, data from 95 scanners were ultimately analyzed. For the first 5:20 min (64 transients), median (interquartile range) drift was 0.44 (1.29) Hz before fMRI and 0.83 (1.29) Hz after. This increased to 3.15 (4.02) Hz for the full 30 min (360 transients) run. Average drift rates were 0.29 Hz/min before fMRI and 0.43 Hz/min after. Paired t-tests indicated that drift increased after fMRI, as expected (p < 0.05). Simulated spectra convolved with the frequency drift showed that the intensity of the NAA singlet was reduced by up to 26%, 44 % and 18% for GE, Philips and Siemens scanners after fMRI, respectively. ICCs indicated good agreement between datasets acquired on separate days. The single site long acquisition showed drift rate was reduced to 0.03 Hz/min approximately three hours after fMRI. Discussion This study analyzed frequency drift data from 95 3T MRI scanners. Median levels of drift were relatively low (5-min average under 1 Hz), but the most extreme cases suffered from higher levels of drift. The extent of drift varied across scanners which both linear and nonlinear drifts were observed.

Data format specification for the NIfTI-MRS file format. NIfTI-MRS is a NIfTI derived format for storing magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. Generated from the specification at the NIfTI-MRS GitHub repository. Documentationfor the format is available online.