Difference between revisions of "SOCR EduMaterials AnalysesCommandLine"
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* [http://www.loni.ucla.edu/twiki/bin/view/CCB/SIGPNS_052109 Example uses of these tools as part of computational neuroimaging pipeline workflows]. | * [http://www.loni.ucla.edu/twiki/bin/view/CCB/SIGPNS_052109 Example uses of these tools as part of computational neuroimaging pipeline workflows]. | ||
Revision as of 01:09, 12 March 2010
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_AnalysesCommandLineVolume2PairedSamples_Wilcoxon_RankSum
- SOCR_EduMaterials_AnalysesCommandLineVolume2Samples_T_test
- SOCR_EduMaterials_AnalysesCommandLineVolume2IndepSample_Wilcoxon_test
- SOCR_EduMaterials_AnalysesCommandLineFDR_Correction
- SOCR_EduMaterials_AnalysesCommandLineVolumeKruskalWallis
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