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Functional magnetic resonance imaging (fMRI) is a standard tool to investigate the neural correlates of cognition. fMRI noninvasively measures brain activity, allowing identification of patterns evoked by tasks performed during scanning. Despite the long history of this technique, the idiosyncrasies of each dataset have led to the use of ad-hoc preprocessing protocols customized for nearly every different study. This approach is time-consuming, error-prone, and unsuitable for combining datasets from many sources. Here we showcasefMRIPrep(http://fmriprep.org), a robust tool to prepare human fMRI data for statistical analysis. This software instrument addresses the reproducibility concerns of the established protocols for fMRI preprocessing. By leveraging the Brain Imaging Data Structure (BIDS) to standardize both the input datasets —MRI data as stored by the scanner— and the outputs —data ready for modeling and analysis—,fMRIPrepis capable of preprocessing a diversity of datasets without manual intervention. In support of the growing popularity offMRIPrep, this protocol describes how to integrate the tool in a task-based fMRI investigation workflow.

The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research. Here, we describe OpenNeuro, a BRAIN Initiative data archive that provides the ability to openly share data from a broad range of brain imaging data types following the FAIR principles for data sharing. We highlight the importance of the Brain Imaging Data Structure standard for enabling effective curation, sharing, and reuse of data. The archive presently shares more than 600 datasets including data from more than 20,000 participants, comprising multiple species and measurement modalities and a broad range of phenotypes. The impact of the shared data is evident in a growing number of published reuses, currently totalling more than 150 publications. We conclude by describing plans for future development and integration with other ongoing open science efforts.

Brain extraction is a ubiquitous initial step in MRI analysis pipelines. Although there are several solutions for human imaging, existing rodent imaging tools often perform poorly on new data with acquisition protocols and parameters that differ from the images with which the tools were developed. Here, we adapted antsBrainExtraction (from the popular ANTs neuroimaging toolbox), which implements atlas-based brain extraction of adult humans, for use with rat MRI data. The new tool, artsBrainExtraction, was evaluated on 190 images from three different scanners, utilising six imaging protocols that differ in contrast, resolution, and field-of-view. The tool produced highly accurate brain masks in 186 (98 %) of the images and adequate masks in the other four. We present a reliable brain extraction tool for rodent images that is agnostic to the imaging protocol and can be extended to further image modalities and non-human populations.

Mapping the causal effects of one brain region on another is a challenging problem in neuroscience that we approached through invasive direct manipulation of brain function together with concurrent whole-brain measurement of the effects produced. Here we establish a unique resource and present data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. We describe the resource, data collection process, preprocessing using the fMRIPrep analysis pipeline and management of artifacts, and provide end-user analyses to visualize distal brain activation produced by site-specific electrical stimulation. The data are organized according to the brain imaging data structure (BIDS) specification, and are available for analysis or future dataset contributions on openneuro.org including both raw and preprocessed data., Measurement(s) brain measurement • anatomical image data • functional brain measurement Technology Type(s) magnetic resonance imaging (MRI) • functional magnetic resonance imaging Factor Type(s) pre-surgery versus post-surgery • electrical stimulation (on vs off) Sample Characteristic - Organism Homo sapiens Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12625541

Background Progress in precision psychiatry is predicated on identifying reliable individual-level diagnostic biomarkers. For psychosis, measures of structural and functional connectivity could be promising biomarkers given consistent reports of dysconnectivity across psychotic disorders using magnetic resonance imaging. Methods We leveraged data from four independent cohorts of patients with psychosis and control subjects with observations from approximately 800 individuals. We used group-level analyses and two supervised machine learning algorithms (support vector machines and ridge regression) to test within-, between-, and across-sample classification performance of white matter and resting-state connectivity metrics. Results Although we replicated group-level differences in brain connectivity, individual-level classification was suboptimal. Classification performance within samples was variable across folds (highest area under the curve [AUC] range = 0.30) and across datasets (average support vector machine AUC range = 0.50; average ridge regression AUC range = 0.18). Classification performance between samples was similarly variable or resulted in AUC values of approximately 0.65, indicating a lack of model generalizability. Furthermore, collapsing across samples (resting-state functional magnetic resonance imaging, N = 888; diffusion tensor imaging, N = 860) did not improve model performance (maximal AUC = 0.67). Ridge regression models generally outperformed support vector machine models, although classification performance was still suboptimal in terms of clinical relevance. Adjusting for demographic covariates did not greatly affect results. Conclusions Connectivity measures were not suitable as diagnostic biomarkers for psychosis as assessed in this study. Our results do not negate that other approaches may be more successful, although it is clear that a systematic approach to individual-level classification with large independent validation samples is necessary to properly vet neuroimaging features as diagnostic biomarkers.

Mapping the causal effects of one brain region on another (effective connectivity) is a challenging problem in neuroscience, since it requires invasive direct manipulation of brain function, together with whole-brain measurement of the effects produced. Here we establish a unique resource and present data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. We describe the resource, data collection process, preprocessing using the fMRIPrep analysis pipeline and management of artifacts, and provide end-user analyses to visualize distal brain activation produced by site-specific electrical stimulation. The data are organized according to the brain imaging data structure (BIDS) specification, and are available for analysis or future dataset contributions on openneuro.org including both raw and preprocessed data.

Quality control of MR images is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. However, the visual inspection of individual images is time-consuming and limited by both intra- and inter-rater variance. The difficulty of visual inspection scales with study size and with the heterogeneity of multi-site data. Here, we describe a tool for the automated assessment of T1-weighted MR images of the brain - MRIQC. MRIQC calculates a set of quality measures from each image and uses them as features in a binary (include/exclude) classifier. The classifier was designed to ensure generalization to new samples acquired in different centers and using different scanning parameters from our training dataset. To achieve that goal, the classifier was trained on the Autism Brain Imaging Data Exchange (ABIDE) dataset (N=1102), acquired at 17 locations with heterogeneous scanning parameters. We selected random forests from a set of models and pre-processing options using nested cross-validation on the ABIDE dataset. We report a performance of ∼89% accuracy of the best model evaluated with nested cross-validation. The best performing classifier was then evaluated on a held-out (unseen) dataset, unrelated to ABIDE and labeled by a different expert, yielding ∼73% accuracy. The MRIQC software package and the trained classifier are released as an open source project, so that individual researchers and large consortia can readily curate their data regardless the size of their databases. Robust QC is crucial to identify early structured imaging artifacts in ongoing acquisition efforts, and helps detect individual substandard images that may bias downstream analyses.

Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain dataset with ground truth white matter tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. While most state-of-the-art algorithms reconstructed 90% of ground truth bundles to at least some extent, on average they produced four times more invalid than valid bundles. About half of the invalid bundles occurred systematically in the majority of submissions. Our results demonstrate fundamental ambiguities inherent to tract reconstruction methods based on diffusion orientation information, with critical consequences for the approach of diffusion tractography in particular and human connectivity studies in general.

Los trastornos del ciclo de la urea suponen hasta el 60% de las hiperamoniemias graves neonatales. La base de los trastornos de este ciclo deriva en el de´ficit de una de sus enzimas. El de´ficit de la enzima ornitina transcarbamilasa es el ma´s frecuente. Su prono´stico dependera´ del grado de deficiencia enzima´tica, la edad, la precocidad del diagno´stico e inicio del tratamiento. Presentamos el caso de un adolescente que, a partir de un cuadro de para´lisis facial perife´rica tratado con prednisona, presento´ agravamiento de su estado general y fallecio´ a los pocos di´as. Las cifras elevadas de amoniaco en sangre hicieron sospechar tardi´amente de una alteracio´n conge´nita del ciclo de la urea, que fue confirmada por su estudio gene´tico post mortem. Se estudiaron los familiares y se asesoro´ a los afectos y portadores. Reflexionamos sobre la importancia de los programas de cribado neonatal y la posibilidad de aplicarlos en la deteccio´n de los errores conge´nitos del metabolismo.

Quantification of neurotransmission Single-Photon Emission Computed Tomography (SPECT) studies of the dopaminergic system can be used to track, stage and facilitate early diagnosis of the disease. The aim of this study was to implement QuantiDOPA, a semi-automatic quantification software of application in clinical routine to reconstruct and quantify neurotransmission SPECT studies using radioligands which bind the dopamine transporter (DAT). To this end, a workflow oriented framework for the biomedical imaging (GIMIAS) was employed. QuantiDOPA allows the user to perform a semiautomatic quantification of striatal uptake by following three stages: reconstruction, normalization and quantification. QuantiDOPA is a useful tool for semi-automatic quantification inDAT SPECT imaging and it has revealed simple and flexible.