@Jim: From Isaiah Norton during 07/23/2013 Devel hangout: This seems like a release blocker to me, is it on the roadmap?: http://www.na-mic.org/Bug/view.php?id=3091

BrainsFit is a separate repository. Not sure I have access to submit a patch directly.

Not seeing anything obvious in the BrainsFit.xml file.

Does data hierarchy get modified correctly in the AffineRegistration module on your system?

@Jim: If needed, you could submit a pull request to https://github.com/BRAINSia/BRAINSTools

I think the problem is between the CLIModuleLogic and the ApplicationLogic. CLIModule logic relies on being able to send a string to the ApplicationLogic via the RequestModified() method. The string is a set of Tcl commands to modify the hierarchy.

I need to dig through some git history.

Looks like this never worked in Slicer4 for any of the registration modules.

There is code in Slicer3 in vtkSlicerApplicationLogic::ProcessModified() that tries to cast the object to a vtkStringArray. If the cast is successful, then it assumes the StringArray is a set of Tcl commands to execute.

Slicer4 does not have this code.

Could you post links to the code that was in charge of placing the moving volume is under the new transform?

The code here used to execute strings passes through RequestModified()

https://github.com/Slicer/Slicer/blob/d597c5204220bea3b961f2746313f2f16eac6dde/Base/Logic/vtkSlicerApplicationLogic.cxx#L1147-L1171

The code that passed the string to reorganize the hierarchy is still in Slicer4

https://github.com/Slicer/Slicer/blob/master/Base/QTCLI/vtkSlicerCLIModuleLogic.cxx#L2135-L2145

I think there used to be other places in Slicer3 where we would pass a string through RequestModified() to trigger a script/string to be executed in the main thread.

If there is not a general way to add back the "string script through RequestModified()" capability, then in this case, we can add specific methods to manage the editing of the hierarchy.

Jc recommended looking at the InvokeEventWithDelay() that was introduced in r22195 and r22196 to communicate the request to reorganize the hierarchy from the processing thread to the gui thread.

To invoke event from a thread, may be the mechanism implemented by Julien could be leveraged:

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22195
and http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22196

Patch r22254 restores the transform hierarchy editing capability that was available in Slicer3 to Slicer4.

Tested on the legacy "RigidRegistration" module.

BrainsFit registration currently crashes for me using the tumor Sample Data for an unrelated reason (down in ITK when loading libraries).

@Jim: Could you work with Hans and provide him instruction to reproduce the crash. Thks

@Jim: Could you have a look at there before the end of the week. The idea would be to cut the 4.3.1 on Monday next week (Sept 23). Thanks

This is now working fine with BrainsFit. Crash issue must have been resolved during a rebuild.

Resolved as in note 9352.

Thanks.