EXtensible Neuroimaging Archive Toolkit (XNAT) Washington University Neuroinformatics Group.
Outline BatchMake Overview BatchMake and XNAT Integration XNAT Overview GridWizard.
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Transcript of Outline BatchMake Overview BatchMake and XNAT Integration XNAT Overview GridWizard.
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Outline
BatchMake Overview BatchMake and XNAT Integration XNAT Overview GridWizard
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BatchMake Overview Goals BatchMake Slicer BatchMake Modules Use-case
High-throughput mouse brain morphology
FundingNIH/NLM A2D2 Award, 2004-2005NAMIC, 2007-2008NIH/NIMH STTR Phase I, High Throughput Web-
Based Image Analysis of Mouse Brain MR Imaging Studies, UNC, PI: M. Styner, 2007-2008
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Goals Facilitate the development and deployment of
scripts for high-throughput image processing Simplify the specification and reporting of
statistical experiments
Use casesDevelop the script using 10 images on a local PC,
and deploy using 1,000s of images on a GridConduct and report a Taguchi experiment to
determine the significant parameters of a methodConduct leave-on-out analyses to compare two
different methods
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BatchMake
Scripting language Editor Processing engines Report Server
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Scripting Language
Modeled after CMakeSet( VAR value )
ListFilesInDir( VAR dir )
ForEach( VAR list )
ForNFold( ITERATION TRAININGSETi
TESTINGSETi fullSet numberOfFolds )
Extensible
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Scripting Language
Applications that use Slicer execution model are available as commands
# Find RegisterImages and determine
# its command-line parameters
Set( @RI RegisterImage )
Set( RI.FixedImage filename)
Set( RI.MovingImage filename)
Set( RI.Registration “Bspline”)
Run( RI )
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Editor
Syntax highlighting Define non-Slicer apps
as commands Launch a processing
engine Monitor results
Loops are unrolled○ Jobs○ Data○ Steps
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Processing Engines
Launched from Editor Launched from command-line
Local processing (bash / bat) Condor Grid Sun Grid KWGrid Globus (limited support)
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Report Server: BatchBoards Script declares an experiment design,
independent vars, dependent vars, thumbnails, and a BatchBoard server
BatchBoard server (website and mysql database) receives data from scripts, provides a database browser, provides experiment reports.
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BatchBoard Reports
Taguchi table webpage
Graphs of independent vs. dependent vars.
Color highlighting when dependent vars passes a threshold
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Slicer Modules (approx.)
Enable BatchMake(automatic with GetBuildTest2)
“Batch Processing” filter groupApplications/CLI/BatchMake
EMSegmenter GaussianBlur (“hello world”)
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High-throughput mouse brain morphology (Phase II) The proposed web-based system with the
server side modules will be evaluated directly by end-users in the following studies:Fragile X mouse behavioral phenotype from
Phase 1,Neuregulin modulated schizophrenia mouse
phenotype,Postnatal alcohol exposure in adolescent mice,Intra-uterine cocaine exposure in rats.
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BatchMake and XNAT
Explore data via XNAT Export pointers to interesting data as an
XNAT Catalog BatchMake commands exist for creating
lists from XNAT Catalogs BatchMake commands exist for
downloading data from XNAT (status?)
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XNAT
Server Desktop File format
for meta-data and data collections
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Grid Wizard
Command-line tool for distributing a program to a variety of compute services