scholarly journals Exploring the Impact of Analysis Software on Task fMRI Results

2018 ◽  
Author(s):  
Alexander Bowring ◽  
Camille Maumet ◽  
Thomas E. Nichols
Keyword(s):  
Software Package ◽  
Similarity Coefficients ◽  
Analysis Software ◽  
Shared Data ◽  
Software Packages ◽  
Fmri Study ◽  
Task Variation ◽  
Scientific Results ◽  
Neuroimaging Software ◽  
The Impact

AbstractA wealth of analysis tools are available to fMRI researchers in order to extract patterns of task variation and, ultimately, understand cognitive function. However, this ‘methodological plurality’ comes with a drawback. While conceptually similar, two different analysis pipelines applied on the same dataset may not produce the same scientific results. Differences in methods, implementations across software packages, and even operating systems or software versions all contribute to this variability. Consequently, attention in the field has recently been directed to reproducibility and data sharing. Neuroimaging is currently experiencing a surge in initiatives to improve research practices and ensure that all conclusions inferred from an fMRI study are replicable.In this work, our goal is to understand how choice of software package impacts on analysis results. We use publically shared data from three published task fMRI neuroimaging studies, reanalyzing each study using the three main neuroimaging software packages, AFNI, FSL and SPM, using parametric and nonparametric inference. We obtain all information on how to process, analyze, and model each dataset from the publications. We make quantitative and qualitative comparisons between our replications to gauge the scale of variability in our results and assess the fundamental differences between each software package. While qualitatively we find broad similarities between packages, we also discover marked differences, such as Dice similarity coefficients ranging from 0.000 - 0.743 in comparisons of thresholded statistic maps between software. We discuss the challenges involved in trying to reanalyse the published studies, and highlight our own efforts to make this research reproducible.

Using of Validated Software for Uncertainty Analyses Tools in Accredited Laboratories

2008 ◽  
Vol 381-382 ◽  
pp. 599-602 ◽  
Author(s):  
O. Velychko
Keyword(s):  
Uncertainty Analysis ◽  
Software Package ◽  
International Standards ◽  
Measuring Instruments ◽  
Analysis Software ◽  
Testing Laboratories ◽  
Software Packages ◽  
Uncertainty Of Measurements ◽  
Accredited Laboratories ◽  
Uncertainty Analyses

According to international standards the accredited calibration and testing laboratories are required to use reliable measuring instruments and to estimate an uncertainty of measurements. The variety of software tools and the different approaches taken will almost certainly ensure that for each laboratory there is a software package which will meet the needs. In this paper, several a software packages are made according to their validation for comparison. Briefly general principles of validating uncertainty analysis software packages are described. Briefly used validation methods are described.

DNA

1995 ◽  
Author(s):  
Peter M. Rice ◽  
Keith EHiston
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Software Package ◽  
Sequence Data ◽  
Sequence Assembly ◽  
Analysis Software ◽  
Considerable Time ◽  
Laboratory Computer ◽  
Software Packages ◽  
Common Laboratory

Software packages are available for all common laboratory computer systems. The packages for personal computers (PC or Macintosh) are able assemble and correct the sequence, those for the larger systems (VAX or Unix) are generally able to analyze the sequence in greater detail. Most laboratories will be able to use sequence assembly programs in their favorite sequence analysis software package. In general, the stages of sequence assembly are gel entry, overlap detection, editing, and reporting. The available programs differ in the ways they handle each of these tasks. No single package is ideal, though all should be adequate for a smaller project such as a single cDNA. Particular attention should be given to the quality and features of the editor, as this is where most time will be spent, and to the possibilities of extending the software to cope with problems that may arise. Good status reports and a choice of methods for overlap detection can save considerable time in resolving ambiguities and correcting errors later. Figure 1 lists some of the commonly used sequence assembly programs. The prices vary widely depending on the features of the package and the options for academic or commercial licenses. Originally, each package used its own “special” codes to represent ambiguous bases and gaps in sequences. Mostpackages now use the standard IUB-IUPAC codes (Figure 2) for the nucleotides, though the program documentation should be checked before starting the project. The task of sequence reading depends on the sequencing protocol used. In many laboratories the sequence is generated on an autoradiograph (Figure 3) from which the sequence is read. Although automated gel readers are on the market, most sequence data is read manually with the aid of a digitizer. Most sequence assembly programs accept DNA sequence read by a sonic digitizer. An example of a device which is supported by most of the available programs is the GrafBar GP-7 [Science Accessories Corporation, Southport, CT, US A and P.M.S. (Instruments) Ltd., Waldeck House, Reform Road, Maidenhead, Berks, SL6 8BX, UK]. Sonic digitizers have a stylus to point to locations on an autoradiograph, which is illuminated from below by a light box.

Impact of pile-to-cap fixity on the design and behavior of sensitive structures

PCI Journal ◽  
2022 ◽  
Vol 67 (1) ◽  
Author(s):  
Isabella Zapata ◽  
John Corven ◽  
Seung Jae Lee ◽  
David Garber
Keyword(s):  
Concrete Strength ◽  
Analysis Software ◽  
Box Girders ◽  
Element Analysis ◽  
Software Packages ◽  
Pile Cap ◽  
Pile Caps ◽  
Embedment Length ◽  
And Behavior ◽  
The Impact

This paper presents the results of analytical studies on the connection between piles and pile caps or footings. Two nonlinear finite element analysis software packages were used to investigate the behavior of the connection itself and the impact of connection assumptions on the overall behavior of different sensitive structures such as simple spans with uneven span lengths, segmental box girders with fixed pier tables, and straddle bents with temperature loading. Results show that the behavior of the connection is affected by variables such as pile size, pile embedment length, pile cap concrete strength, interface reinforcement, and distance between the edge of the pile and the edge of the pile cap. The study also demonstrated that significant moment can develop even with shallow pile embedment lengths. The assumed level of fixity between the pile and pile cap was found to significantly influence the behavior of some of the bridges investigated in this study.

scholarly journals Sharing brain mapping statistical results with the neuroimaging data model

2016 ◽  
Author(s):  
Camille Maumet ◽  
Tibor Auer ◽  
Alexander Bowring ◽  
Gang Chen ◽  
Samir Das ◽  
...  
Keyword(s):  
Data Model ◽  
Image Data ◽  
Software Packages ◽  
Fmri Study ◽  
Neuroimaging Data ◽  
Neuroimaging Software ◽  
Meta Analyses ◽  
Machine Readable ◽  
Univariate Analyses ◽  
Statistical Results

AbstractOnly a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html.

Influence of the distribution of the shear walls on the seismic response of the buildings

2020 ◽  
Vol 15 (1) ◽  
pp. 37-44
Author(s):  
El Mehdi Echebba ◽  
Hasnae Boubel ◽  
Oumnia Elmrabet ◽  
Mohamed Rougui
Keyword(s):  
Structural Analysis ◽  
Seismic Response ◽  
Natural Frequency ◽  
Structural Design ◽  
Structural Response ◽  
Shear Walls ◽  
Structural Elements ◽  
Analysis Software ◽  
Ansys Apdl ◽  
The Impact

Abstract In this paper, an evaluation was tried for the impact of structural design on structural response. Several situations are foreseen as the possibilities of changing the distribution of the structural elements (sails, columns, etc.), the width of the structure and the number of floors indicates the adapted type of bracing for a given structure by referring only to its Geometric dimensions. This was done by studying the effect of the technical design of the building on the natural frequency of the structure with the study of the influence of the distribution of the structural elements on the seismic response of the building, taking into account of the requirements of the Moroccan earthquake regulations 2000/2011 and using the ANSYS APDL and Robot Structural Analysis software.

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