Pypes: Workflows for Processing Multimodal Neuroimaging Data

Project, toolkit, and database of neuroinformatics ecosystem: A summary of previous studies on "Frontiers in Neuroinformatics"

In the field of neuroscience, the core of the cohort study project consists of collection, analysis, and sharing of multi-modal data. Recent years have witnessed a host of efficient and high-quality toolkits published and employed to improve the quality of multi-modal data in the cohort study. In turn, gleaning answers to relevant questions from such a conglomeration of studies is a time-consuming task for cohort researchers. As part of our efforts to tackle this problem, we propose a hierarchical neuroscience knowledge base that consists of projects/organizations, multi-modal databases, and toolkits, so as to facilitate researchers' answer searching process. We first classified studies conducted for the topic "Frontiers in Neuroinformatics" according to the multi-modal data life cycle, and from these studies, information objects as projects/organizations, multi-modal databases, and toolkits have been extracted. Then, we map these information objects into our proposed knowledge base framework. A Python-based query tool has also been developed in tandem for quicker access to the knowledge base, (accessible at https://github.com/Romantic-Pumpkin/PDT_fninf). Finally, based on the constructed knowledge base, we discussed some key research issues and underlying trends in different stages of the multi-modal data life cycle.

ENIGMA HALFpipe: Interactive, reproducible, and efficient analysis for resting-state and task-based fMRI data

The reproducibility crisis in neuroimaging has led to an increased demand for standardized data processing workflows. Within the ENIGMA consortium, we developed HALFpipe (Harmonized Analysis of Functional MRI pipeline), an open-source, containerized, user-friendly tool that facilitates reproducible analysis of task-based and resting-state fMRI data through uniform application of preprocessing, quality assessment, single-subject feature extraction, and group-level statistics. It provides state-of-the-art preprocessing using fMRIPrep without the requirement for input data in Brain Imaging Data Structure (BIDS) format. HALFpipe extends the functionality of fMRIPrep with additional preprocessing steps, which include spatial smoothing, grand mean scaling, temporal filtering, and confound regression. HALFpipe generates an interactive quality assessment (QA) webpage to rate the quality of key preprocessing outputs and raw data in general. HALFpipe features myriad post-processing functions at the individual subject level, including calculation of task-based activation, seed-based connectivity, network-template (or dual) regression, atlas-based functional connectivity matrices, regional homogeneity (ReHo), and fractional amplitude of low-frequency fluctuations (fALFF), offering support to evaluate a combinatorial number of features or preprocessing settings in one run. Finally, flexible factorial models can be defined for mixed-effects regression analysis at the group level, including multiple comparison correction. Here, we introduce the theoretical framework in which HALFpipe was developed, and present an overview of the main functions of the pipeline. HALFpipe offers the scientific community a major advance toward addressing the reproducibility crisis in neuroimaging, providing a workflow that encompasses preprocessing, post-processing, and QA of fMRI data, while broadening core principles of data analysis for producing reproducible results. Instructions and code can be found at https://github.com/HALFpipe/HALFpipe.

mGluR 5 and GABA A receptor‐specific parametric PET atlas construction— PET / MR data processing pipeline, validation, and application

The glutamate and γ‐aminobutyric acid neuroreceptor subtypes mGluR₅ and GABA_A are hypothesized to be involved in the development of a variety of psychiatric diseases. However, detailed information relating to their in vivo distribution is generally unavailable. Maps of such distributions could potentially aid clinical studies by providing a reference for the normal distribution of neuroreceptors and may also be useful as covariates in advanced functional magnetic resonance imaging (MR) studies. In this study, we propose a comprehensive processing pipeline for the construction of standard space, in vivo distributions of non‐displaceable binding potential (BP_ND), and total distribution volume (V_T) based on simultaneously acquired bolus‐infusion positron emission tomography (PET) and MR data. The pipeline was applied to [¹¹C]ABP688‐PET/MR (13 healthy male non‐smokers, 26.6 ± 7.0 years) and [¹¹C]Flumazenil‐PET/MR (10 healthy males, 25.8 ± 3.0 years) data. Activity concentration templates, as well as V_T and BP_ND atlases of mGluR₅ and GABA_A, were generated from these data. The maps were validated by assessing the percent error δ from warped space to native space in a selection of brain regions. We verified that the average δ_ABP = 3.0 ± 1.0% and δ_FMZ = 3.8 ± 1.4% were lower than the expected variabilities σ of the tracers (σ_ABP = 4.0%–16.0%, σ_FMZ = 3.9%–9.5%). An evaluation of PET‐to‐PET registrations based on the new maps showed higher registration accuracy compared to registrations based on the commonly used [¹⁵O]H₂O‐template distributed with SPM12. Thus, we conclude that the resulting maps can be used for further research and the proposed pipeline is a viable tool for the construction of standardized PET data distributions.

Mapping covariance in brain FDG uptake to structural connectivity

PURPOSE

Inter-subject covariance of regional 18F-fluorodeoxyglucose (FDG) PET measures (FDG_cov) as proxy of brain connectivity has been gaining an increasing acceptance in the community. Yet, it is still unclear to what extent FDG_cov is underlied by actual structural connectivity via white matter fiber tracts. In this study, we quantified the degree of spatial overlap between FDG_cov and structural connectivity networks.

METHODS

We retrospectively analyzed neuroimaging data from 303 subjects, both patients with suspected neurodegenerative disorders and healthy individuals. For each subject, structural magnetic resonance, diffusion tensor imaging, and FDG-PET data were available. The images were spatially normalized to a standard space and segmented into 62 anatomical regions using a probabilistic atlas. Sparse inverse covariance estimation was employed to estimate FDG_cov. Structural connectivity was measured by streamline tractography through fiber assignment by continuous tracking.

RESULTS

For the whole brain, 55% of detected connections were found to be convergent, i.e., present in both FDG_cov and structural networks. This metric for random networks was significantly lower, i.e., 12%. Convergent were 80% of intralobe connections and only 30% of interhemispheric interlobe connections.

CONCLUSION

Structural connectivity via white matter fiber tracts is a relevant substrate of FDG_cov, underlying around a half of connections at the whole brain level. Short-range white matter tracts appear to be a major substrate of intralobe FDG_cov connections.

Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI, and PET data), as well as tools for statistics, machine learning, and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS, and NIFD). Processed data include image-valued scalar fields (e.g., tissue probability maps), meshes, surface-based scalar fields (e.g., cortical thickness maps), or scalar outputs (e.g., regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.

Integrity of Neurocognitive Networks in Dementing Disorders as Measured with Simultaneous PET/Functional MRI

Functional MRI (fMRI) studies have reported altered integrity of large-scale neurocognitive networks (NCNs) in dementing disorders. However, findings on the specificity of these alterations in patients with Alzheimer disease (AD) and behavioral-variant frontotemporal dementia (bvFTD) are still limited. Recently, NCNs have been successfully captured using PET with ¹⁸F-FDG. Methods: Network integrity was measured in 72 individuals (38 male) with mild AD or bvFTD, and in healthy controls, using a simultaneous resting-state fMRI and ¹⁸F-FDG PET. Indices of network integrity were calculated for each subject, network, and imaging modality. Results: In either modality, independent-component analysis revealed 4 major NCNs: anterior default-mode network (DMN), posterior DMN, salience network, and right central executive network (CEN). In fMRI data, the integrity of the posterior DMN was found to be significantly reduced in both patient groups relative to controls. In the AD group the anterior DMN and CEN appeared to be additionally affected. In PET data, only the integrity of the posterior DMN in patients with AD was reduced, whereas 3 remaining networks appeared to be affected only in patients with bvFTD. In a logistic regression analysis, the integrity of the anterior DMN as measured with PET alone accurately differentiated between the patient groups. A correlation between indices of 2 imaging modalities was low overall. Conclusion: FMRI and ¹⁸F-FDG PET capture partly different aspects of network integrity. A higher disease specificity for NCNs as derived from PET data supports metabolic connectivity imaging as a promising diagnostic tool.

APPIAN: Automated Pipeline for PET Image Analysis

APPIAN is an automated pipeline for user-friendly and reproducible analysis of positron emission tomography (PET) images with the aim of automating all processing steps up to the statistical analysis of measures derived from the final output images. The three primary processing steps are coregistration of PET images to T1-weighted magnetic resonance (MR) images, partial-volume correction (PVC), and quantification with tracer kinetic modeling. While there are alternate open-source PET pipelines, none offers all of the features necessary for making automated PET analysis as reliably, flexibly and easily extendible as possible. To this end, a novel method for automated quality control (QC) has been designed to facilitate reliable, reproducible research by helping users verify that each processing stage has been performed as expected. Additionally, a web browser-based GUI has been implemented to allow both the 3D visualization of the output images, as well as plots describing the quantitative results of the analyses performed by the pipeline. APPIAN also uses flexible region of interest (ROI) definition—with both volumetric and, optionally, surface-based ROI—to allow users to analyze data from a wide variety of experimental paradigms, e.g., longitudinal lesion studies, large cross-sectional population studies, multi-factorial experimental designs, etc. Finally, APPIAN is designed to be modular so that users can easily test new algorithms for PVC or quantification or add entirely new analyses to the basic pipeline. We validate the accuracy of APPIAN against the Monte-Carlo simulated SORTEO database and show that, after PVC, APPIAN recovers radiotracer concentrations within 93–100% accuracy.

How random is the random forest? Random forest algorithm on the service of structural imaging biomarkers for Alzheimer's disease: from Alzheimer's disease neuroimaging initiative (ADNI) database

Neuroinformatics is a fascinating research field that applies computational models and analytical tools to high dimensional experimental neuroscience data for a better understanding of how the brain functions or dysfunctions in brain diseases. Neuroinformaticians work in the intersection of neuroscience and informatics supporting the integration of various sub-disciplines (behavioural neuroscience, genetics, cognitive psychology, etc.) working on brain research. Neuroinformaticians are the pathway of information exchange between informaticians and clinicians for a better understanding of the outcome of computational models and the clinical interpretation of the analysis. Machine learning is one of the most significant computational developments in the last decade giving tools to neuroinformaticians and finally to radiologists and clinicians for an automatic and early diagnosis-prognosis of a brain disease. Random forest (RF) algorithm has been successfully applied to high-dimensional neuroimaging data for feature reduction and also has been applied to classify the clinical label of a subject using single or multi-modal neuroimaging datasets. Our aim was to review the studies where RF was applied to correctly predict the Alzheimer's disease (AD), the conversion from mild cognitive impairment (MCI) and its robustness to overfitting, outliers and handling of non-linear data. Finally, we described our RF-based model that gave us the 1st position in an international challenge for automated prediction of MCI from MRI data.