Dataset Information

A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines.

ABSTRACT: In recent years, the replicability of neuroimaging findings has become an important concern to the research community. Neuroimaging pipelines consist of myriad numerical procedures, which can have a cumulative effect on the accuracy of findings. To address this problem, we propose a method for simulating artificial lesions in the brain in order to estimate the sensitivity and specificity of lesion detection, using different automated corticometry pipelines. We have applied this method to different versions of two widely used neuroimaging pipelines (CIVET and FreeSurfer), in terms of coefficients of variation; sensitivity and specificity of detecting lesions in 4 different regions of interest in the cortex, while introducing variations to the lesion size, the blurring kernel used prior to statistical analyses, and different thickness metrics (in CIVET). These variations are tested in a between-subject design (in two random groups, with and without lesions, using T1-weigted MRIs of 152 individuals from the International Consortium of Brain Mapping (ICBM) dataset) and in a within-subject pre-/post-lesion design [using 21 T1-Weighted MRIs of a single adult individual, scanned in the Infant Brain Imaging Study (IBIS)]. The simulation method is sensitive to partial volume effect and lesion size. Comparisons between pipelines illustrate the ability of this method to uncover differences in sensitivity and specificity of lesion detection. We propose that this method be adopted in the workflow of software development and release.

SUBMITTER: OmidYeganeh M

PROVIDER: S-EPMC8350777 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines.

OmidYeganeh Mona M Khalili-Mahani Najmeh N Bermudez Patrick P Ross Alison A Lepage Claude C Vincent Robert D RD Jeon S S Lewis Lindsay B LB Das S S Zijdenbos Alex P AP Rioux Pierre P Adalat Reza R Van Eede Matthijs C MC Evans Alan C AC

Frontiers in neuroinformatics 20210726

In recent years, the replicability of neuroimaging findings has become an important concern to the research community. Neuroimaging pipelines consist of myriad numerical procedures, which can have a cumulative effect on the accuracy of findings. To address this problem, we propose a method for simulating artificial lesions in the brain in order to estimate the sensitivity and specificity of lesion detection, using different automated corticometry pipelines. We have applied this method to differe ...[more]

PMID: 34381348

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Project description:BackgroundBioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts.ResultsTo enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats).ConclusionsPaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples.

Project description:Objective. X-ray-based imaging modalities including mammography and computed tomography (CT) are widely used in cancer screening, diagnosis, staging, treatment planning, and therapy response monitoring. Over the past few decades, improvements to these modalities have resulted in substantially improved efficacy and efficiency, and substantially reduced radiation dose and cost. However, such improvements have evolved more slowly than would be ideal because lengthy preclinical and clinical evaluation is required. In many cases, new ideas cannot be evaluated due to the high cost of fabricating and testing prototypes. Wider availability of computer simulation tools could accelerate development of new imaging technologies. This paper introduces the development of a new open-access simulation environment for x-ray-based imaging. The main motivation of this work is to publicly distribute a fast but accurate ray-tracing x-ray and CT simulation tool along with realistic phantoms and 3D reconstruction capability, building on decades of developments in industry and academia.Approach. The x-ray-based Cancer Imaging Simulation Toolkit (XCIST) is developed in the context of cancer imaging, but can more broadly be applied. XCIST is physics-based, written in Python and C/C++, and currently consists of three major subsets: digital phantoms, the simulator itself (CatSim), and image reconstruction algorithms; planned future features include a fast dose-estimation tool and rigorous validation. To enable broad usage and to model and evaluate new technologies, XCIST is easily extendable by other researchers. To demonstrate XCIST's ability to produce realistic images and to show the benefits of using XCIST for insight into the impact of separate physics effects on image quality, we present exemplary simulations by varying contributing factors such as noise and sampling.Main results. The capabilities and flexibility of XCIST are demonstrated, showing easy applicability to specific simulation problems. Geometric and x-ray attenuation accuracy are shown, as well as XCIST's ability to model multiple scanner and protocol parameters, and to attribute fundamental image quality characteristics to specific parameters.Significance. This work represents an important first step toward the goal of creating an open-access platform for simulating existing and emerging x-ray-based imaging systems. While numerous simulation tools exist, we believe the combined XCIST toolset provides a unique advantage in terms of modeling capabilities versus ease of use and compute time. We publicly share this toolset to provide an environment for scientists to accelerate and improve the relevance of their research in x-ray and CT.

Dataset Information

A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines.

Publications

A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines.

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