In MIPAV, the OAR algorithm can detect whether your input is a set of 2D images or a single 3D volume, and then it will provide the user with the appropriate parameter settings (Rigid - 3 for 2D as opposed to Rigid-6 for 3D, bilinear interpolation instead of trilinear, etc). Can somebody set up a JIST module to handle 2D registration? Perhaps it could be an updated version of OAR where one can set 2D vs 3D registration with the appropriate degrees of freedom, cost function, and interpolation settings.

I re-installed JIST 2.0 because I think there was an issue with this module after trying to install the jist jar compiled from the cvs. I now get the following error, which I think is attributable to the way the dialog is setup in MIPAV:

edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher: Remove.
edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParserRuntime Exception:null
java.lang.NullPointerException
at gov.nih.mipav.view.dialogs.JDialogRegistrationOAR2D.getOutputImageName(JDialogRegistrationOAR2D.java:2933)
at edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser.execute(MipavPluginParser.java:329)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:291)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:275)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog.callAlgorithm(ProcessingDialog.java:261)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog.clickOk(ProcessingDialog.java:301)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.execute(PipeRunner.java:167)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.invoke(PipeRunner.java:250)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.run(PipeRunner.java:102)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.main(PipeRunner.java:59)
edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation Monitor not running. Punting stop.
edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher stopping via interrupt.
edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher finished.
Optimized automatic 2d image registration could not save information.

It looks like the adapter is looking for the output name parameter, likely in a separate dialog prompt in MIPAV, which is not set by the module prior to runtime through JIST.

I tried the adapter under the MIPAV category (Optimized Automatic 2d image registration (5.2.1 R) but I get the following error:

edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParserRuntime Exception:null
Error retrieving parameter: input_image_2: null
at gov.nih.mipav.model.scripting.parameters.ParameterTable.getImage(ParameterTable.java:193)
at gov.nih.mipav.view.dialogs.AlgorithmParameters.retrieveImage(AlgorithmParameters.java:251)
at gov.nih.mipav.view.dialogs.AlgorithmParameters.retrieveInputImage(AlgorithmParameters.java:273)
at gov.nih.mipav.view.dialogs.JDialogRegistrationOAR2D.setGUIFromParams(JDialogRegistrationOAR2D.java:1251)
at gov.nih.mipav.view.dialogs.JDialogScriptableBase.scriptRun(JDialogScriptableBase.java:205)
at edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser.execute(MipavPluginParser.java:296)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:281)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:265)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog.callAlgorithm(ProcessingDialog.java:261)
at edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog.clickOk(ProcessingDialog.java:301)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.execute(PipeRunner.java:166)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.invoke(PipeRunner.java:230)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.run(PipeRunner.java:101)
at edu.jhu.ece.iacl.jist.pipeline.PipeRunner.main(PipeRunner.java:58)
edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation Monitor not running. Punting stop.
edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher stopping via interrupt.
edu.jhu.ece.iacl.jist.pipeline.view.input.RefresherRefresher finished.
Optimized automatic 2d image registration could not save information.

I get this despite having both input images set, which is strange to see that it is interpreting input_image_2 as null. Here is the standard out:

MIPAV STARTED with forceQuite set as true
edu.jhu.ece.iacl.jist.pipeline.PipeRunner Found Class class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
IN: input_image_1 false ext_image null
IN: input_image_2 false ext_image null
IN: do_use_weight_images false boolean false
IN: input_weight_image false ext_image null
IN: reference_weight_image false ext_image null
IN: degrees_of_freedom false int 6
IN: initial_interpolation_type false int 1
IN: cost_function_type false int 1
IN: rotate_begin false float -30.0
IN: rotate_end false float 30.0
IN: coarse_rate false float 15.0
IN: fine_rate false float 6.0
IN: do_display_transform false boolean true
IN: final_interpolation_type false int 1
IN: do_subsample false boolean true
IN: out_of_bounds_index false int 0
OUT: result_image image null
edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory Reading C:\Users\sheacd\Documents\PipelineOut\EyeRegTest\exp-0000\exp-0000-A.input
edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog **************************************************************************
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 0.26 sec / CPU: 0.20 sec

TOTAL ELAPSED TIME: Actual: 0.26 sec / CPU: 0.20 sec
CURRENT MEMORY: Used 8 MB, Free 4 MB, Total 12 MB
edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog SaveAll Failing: Not ready

The module also seems to want weighting images specified or else the Status reports "not ready", whether or not "do_use_weight_images" is checked.

The current 3D model is up in open source and should be reasonable to modify... does the adapter plugin under the "mipav" category meet your needs?