Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics

Budin, François; Hoogstoel, Marion; Reynolds, Patrick; Grauer, Michael; O’Leary‐Moore, Shonagh K.; Oguz, Ipek

doi:10.3389/fninf.2013.00015

Cited by 24 publications

(19 citation statements)

References 57 publications

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“…Therefore, skull-stripping of the input data should become standard, but not only for clinical studies. It can be performed either as a separate step or by inclusion in standard analysis pipelines, as already suggested for non-human data (Budin et al, 2013). Our implementation of skull-stripping with the BET2 software requires considerable manual postprocessing to obtain optimal removal of non-brain areas.…”

Section: Discussionmentioning

confidence: 99%

The benefits of skull stripping in the normalization of clinical fMRI data

Fischmeister

Höllinger

Klinger

et al. 2013

NeuroImage: Clinical

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Establishing a reliable correspondence between lesioned brains and a template is challenging using current normalization techniques. The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed. Here we provide a first investigation into whether clinical fMRI benefits from skull stripping, based on data from a presurgical language localization task. Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches. Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space — particularly when used in combination with the New Segment normalization technique.

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Section: Discussionmentioning

confidence: 99%

The benefits of skull stripping in the normalization of clinical fMRI data

Fischmeister

Höllinger

Klinger

et al. 2013

NeuroImage: Clinical

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“…The data were processed using an in-house pipeline consisting of unbiased, atlas based, regional segmentation (Budin et al, 2013). The images were rigidly aligned (translation and rotation) (Johnson et al, 2007) to an external template for the C57 mouse (The C57 Brookhaven Atlas, Ma et al, 2005) and then skull-stripped using an atlas-based tissue classification method (Oguz et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

Acute alcohol exposure during neurulation: Behavioral and brain structural consequences in adolescent C57BL/6J mice

Fish¹,

Holloway²,

Rumple³

et al. 2016

Behavioural Brain Research

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Prenatal alcohol exposure (PAE) can induce physical malformations and behavioral abnormalities that depend in part on the developmental timing of alcohol exposure. The current studies employed a mouse FASD model to characterize the long-term behavioral and brain structural consequences of a binge-like alcohol exposure during neurulation; a first-trimester stage when women are typically unaware that they are pregnant. Time-mated C57BL/6J female mice were administered two alcohol doses (2.8 g/kg, four hours apart) or vehicle starting at gestational day 8.0. Male and female adolescent offspring (postnatal day28–45) were then examined for motor activity (open field and elevated plus maze), coordination (rotarod), spatial learning and memory (Morris water maze), sensory motor gating (acoustic startle and prepulse inhibition), sociability (three-chambered social test), and nociceptive responses (hot plate). Regional brain volumes and shapes were determined using magnetic resonance imaging. In males, PAE increased activity on the elevated plus maze and reduced social novelty preference, while in females PAE increased exploratory behavior in the open field and transiently impaired rotarod performance. In both males and females, PAE modestly impaired Morris water maze performance and decreased the latency to respond on the hot plate. There were no brain volume differences; however, significant shape differences were found in the cerebellum, hypothalamus, striatum, and corpus callosum. These results demonstrate that alcohol exposure during neurulation can have functional consequences into adolescence, even in the absence of significant brain regional volumetric changes. However, PAE-induced regional shape changes provide evidence for persistent brain alterations and suggest alternative clinical diagnostic markers.

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“…This pipeline and the results of running it on our input datasets are described in detail in (Budin et al, 2013). This composite pipeline is composed of six smaller pipelines, and can process DWI, DTI and structural MRI data.…”

Section: Resultsmentioning

confidence: 99%

A midas plugin to enable construction of reproducible web-based image processing pipelines

Grauer

Reynolds

Hoogstoel

et al. 2013

Front. Neuroinform.

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Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.

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Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics

Cited by 24 publications

References 57 publications

The benefits of skull stripping in the normalization of clinical fMRI data

The benefits of skull stripping in the normalization of clinical fMRI data

Acute alcohol exposure during neurulation: Behavioral and brain structural consequences in adolescent C57BL/6J mice

A midas plugin to enable construction of reproducible web-based image processing pipelines

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