SOCR EduMaterials AnalysesCommandLine

This page includes the information on how to access the SOCR Analyses libraries for statistical computing via shell-based command-line interface on local machines. More information about SOCR Analyses is available here.

Introduction

In addition to the graphical user interfaces, via a web-browser, all SOCR Analyses allow command-line shell execution on local systems.

General Usage

• Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/).
• The command-line interface to SOCR Analyses generally uses EXAMPLE 1 from the list of example data files for the corresponding analysis.
• All Input files are ASCII (see examples within each of the specific analyses).
• a -h flag at the end of the command-line indicates that the first row in all ASCII input data files is a HEADER row (so it's not interpreted as data).
• When running large Java jobs on Grid architectures or when submitting jobs via qsub, the following specification to request additional memory may be useful to avoid OutOfMemoryExceptions: h_vmem=4.5G:

qsub -q short.q -t 1:12 -l h_vmem=4.5G,h_stack=10M VolumeMultipleRegression_FA.tcsh

Analysis-specific Usage

• SOCR_EduMaterials_AnalysesCommandLineAnovaOneWay
• SOCR_EduMaterials_AnalysesCommandLineAnovaTwoWay
• SOCR_EduMaterials_AnalysesCommandLineChiSquareContingencyTable
• SOCR_EduMaterials_AnalysesCommandLineChiSquareModelFit
• SOCR_EduMaterials_AnalysesCommandLineDichotomousProportion
• SOCR_EduMaterials_AnalysesCommandLineFisherExact
• SOCR_EduMaterials_AnalysesCommandLineFlignerKilleen
• SOCR_EduMaterials_AnalysesCommandLineKolmogorovSmirnoff
• SOCR_EduMaterials_AnalysesCommandLineMultiRegression
• SOCR_EduMaterials_AnalysesCommandLineOneT
• SOCR_EduMaterials_AnalysesCommandLineTwoIndependentFriedman
• SOCR_EduMaterials_AnalysesCommandLineTwoIndependentKruskalWallis
• SOCR_EduMaterials_AnalysesCommandLineTwoIndependentTest
• SOCR_EduMaterials_AnalysesCommandLineTwoIndependentWilcoxon
• SOCR_EduMaterials_AnalysesCommandLineTwoPairedSignedTest
• SOCR_EduMaterials_AnalysesCommandLineTwoPairedT
• SOCR_EduMaterials_AnalysesCommandLineTwoPairSignedRank
• SOCR_EduMaterials_AnalysesCommandLineSimpleRegression

Specific Volumetric Analyses

• SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression
• SOCR_EduMaterials_AnalysesCommandLineVolume1Sample_T_test
• SOCR_EduMaterials_AnalysesCommandLineVolume2Samples_T_test
• SOCR_EduMaterials_AnalysesCommandLineVolume2IndepSample_Wilcoxon_test
• SOCR_EduMaterials_AnalysesCommandLineFDR_Correction

• Example uses of these tools as part of computational neuroimaging pipeline workflows.

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