NONINTERACTIVE TOOLS Outline Batch Make Overview Batch Make
NON-INTERACTIVE TOOLS
Outline � Batch. Make Overview � Batch. Make and XNAT Integration � XNAT Overview � Grid. Wizard
Batch. Make Overview � � Goals Batch. Make Slicer Batch. Make Modules Use-case �High-throughput mouse brain morphology � Funding �NIH/NLM A 2 D 2 Award, 2004 -2005 �NAMIC, 2007 -2008 �NIH/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 cases � Develop the script using 10 images on a local PC, and deploy using 1, 000 s of images on a Grid � Conduct and report a Taguchi experiment to determine the significant parameters of a method � Conduct leave-on-out analyses to compare two different methods
Batch. Make � Scripting language � Editor � Processing engines � Report Server
Scripting Language � Modeled after CMake Set( VAR value ) List. Files. In. Dir( VAR dir ) For. Each( VAR list ) For. NFold( ITERATION TRAININGSETi TESTINGSETi full. Set number. Of. Folds ) � Extensible
Scripting Language � Applications that use Slicer execution model are available as commands # Find Register. Images and determine # its command-line parameters Set( @RI Register. Image ) Set( RI. Fixed. Image filename) Set( RI. Moving. Image 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: Batch. Boards � Script declares an experiment design, independent vars, thumbnails, and a Batch. Board server � Batch. Board server (website and mysql database) receives data from scripts, provides a database browser, provides experiment reports.
Batch. Board Reports � Taguchi table webpage � Graphs of independent vs. dependent vars. � Color highlighting when dependent vars passes a threshold
Slicer Modules (approx. ) � Enable Batch. Make �(automatic with Get. Build. Test 2) � “Batch Processing” filter group �Applications/CLI/Batch. Make � EMSegmenter � Gaussian. Blur (“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.
Batch. Make and XNAT � Explore data via XNAT � Export pointers to interesting data as an XNAT Catalog � Batch. Make commands exist for creating lists from XNAT Catalogs � Batch. Make 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
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