View source for Engineering:ITK Grid Pipeline

= Sample Executable =

[[Media:Grid-reg.tar.gz| This tar file]] includes the following:

* '''go''' :
** a simple shell script that runs the registration
** look at it to see the syntax for other data
* '''mrt.img, mrt.nhdr, reg.img, reg.nhdr''' :
** sample data
* '''MultiModalityRigidRegistration''' :
** a statically linked linux x86 executable of this code from the NA-MIC svn Sandbox [http://www.na-mic.org:8000/websvn/listing.php?repname=NAMICSandBox&path=%2FNonRigidRegistrationForEchoPlanarImaging%2F&rev=0&sc=0 here].
* '''xformIN'''
** an initial set of parameters

<br /> The executable is compiled to accept 3D volume datasets (in any of the formats ITK accepts) and write out nrrd format files.

NA-MIC structural MR data in nrrd format is [https://portal.nbirn.net/BIRN/cgi-bin/DataGrid/browse.cgi?browseloc=/home/Projects/NAMIC__0003/Files/Harvard/archive_morph here].

* There are 188 data sets
* An interesting test would be to select a random case as the reference (say, the first case) and register all 187 others to that reference case.
* Note that there are many registration parameters embedded in the ITK executable and once we get the grid process in place, we'll want to optimize the parameters to work well on this data.

= Pipeline Wrapping =

* Please make sure that you have the latest Pipeline (version 3.0) build, available at: [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/BleedingEdgeBuild [1]]

* Download the Pipeline module here: [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/ITKMultiModalityRigidRegistrationModule [2]]

* A presentation with detailed screenshots (on how to load, modify and execute the module) is available here:

[[Media:MMRR_Beta2.0.ppt| Slideshow (with screenshots) for MultiModalityRigidRegistration.module]]

* Please read the following instructions before attempting to run the module

# Make sure You are running Pipeline Version 3.0
# Download MultiModalityRigidRegistration.module
# Run Pipeline (follow instructions on the Wiki)
# Click on Workspace
# Click on Load
# Navigate through directories and load the module
# CHANGING THE URL for the EXECUTABLE
## Right-Click on Module (which says MultiModalityRigidRegistration)
## Choose 'Edit Function' from the right-clicked menu
## A modal dialog named "Edit function: MultiModalityRigidRegistration" will popup
## Click on the ellipsis found at the end of URL field
## Click on the enabled ellipsis, it allows you to browse and edit the URL value
## A popup with title "choose a file" opens up
## Click on ellipsis (at the end of PATH field) to browse
## The drop down menu will show "Pipeline v3 modules" by default, choose "All files" from the menu
## Now browse through directories and choose the file named "MultiModalityRigidRegistration"
# CHANGING THE INPUT DIRECTORY
## Click on Variables Tab
## Expand Input Directory Tab
## Click on the right column for row named "Value 1"
## When you click on the column, ellipsis at the end will be enabled
## Click on the enabled ellipsis, it allows you to browse and edit the value
## A popup with title "compose value" opens up
## Replace "/home/jrajendi/ProgrammersWeek/ItkGridPipeline/testdir/grid-reg/" with Input directory
### Eg: If your input directory is "/home/myinputdirectory" Then, Make sure the url says "pipeline://localhost//home/myinputdirectory"
# CHANGING THE OUTPUT DIRECTORY
## Click on Variables Tab
## Expand Input Directory Tab
## Click on the right column for row named "Value 1"
## When you click on the column, ellipsis at the end will be enabled
## Click on the enabled ellipsis, it allows you to browse and edit the value
## A popup with title "compose value" opens up
## Replace "/home/jrajendi/ProgrammersWeek/ItkGridPipeline/testdir/grid-reg/refinedmodule/" with the Output directory in which you want the .nrrd and xformOUT files to be generated.
### Eg: If your ouput directory is "/home/myouputdirectory" Then, Make sure the url says "pipeline://localhost//home/myoutputdirectory"
# Congratulations, you are now ready to run!
## Click on Execution
## Click on Run
# Runtime status
## The module status should read "child processes started"
# When the module completes, the status will change to "module completed cleanup"
# The module takes an estimated 60 minutes to complete and generate all output files.

= Grid Job Launching =

A full description of this project can be found [[Engineering:Project:Condor_Job_Submission|on the Condor Project Page]]

= Visualizing / Verifying the Results =

[[Media:Grid-reg-after.tar.gz|This tar file]] contains the state of the directory after running the executable.

= Application to Core 3 Biological Goals =