Outline BatchMake Overview BatchMake and XNAT Integration XNAT Overview GridWizard

Outline

BatchMake Overview BatchMake and XNAT Integration XNAT Overview GridWizard

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

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

BatchMake

Scripting language Editor Processing engines Report Server

Scripting Language

Modeled after CMakeSet( VAR value )

ListFilesInDir( VAR dir )

ForEach( VAR list )

ForNFold( ITERATION TRAININGSETi

TESTINGSETi fullSet numberOfFolds )

Extensible

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 )

Editor

Syntax highlighting Define non-Slicer apps

as commands Launch a processing

engine Monitor results

Loops are unrolled○ Jobs○ Data○ Steps

Processing Engines

Launched from Editor Launched from command-line

Local processing (bash / bat) Condor Grid Sun Grid KWGrid Globus (limited support)

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.

BatchBoard Reports

Taguchi table webpage

Graphs of independent vs. dependent vars.

Color highlighting when dependent vars passes a threshold

Slicer Modules (approx.)

Enable BatchMake(automatic with GetBuildTest2)

“Batch Processing” filter groupApplications/CLI/BatchMake

EMSegmenter GaussianBlur (“hello world”)

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.

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?)

XNAT

Server Desktop File format

for meta-data and data collections

Grid Wizard

Command-line tool for distributing a program to a variety of compute services