Error with new extension Elastix

Support
1

Operating system:MacOS 10.12.4
Slicer version:Slicer-4.7.0-2017-05-02-macosx-amd64
Expected behavior:successful registration between two volume
Actual behavior:“KeyError: ‘LD_LIBRARY_PATH’”
Hey there, I am trying to register with this new extension Elastix. I have installed the extension and the Elastix toolbox from its official website. I can call elastix successfully in the terminal. However, when I am trying to register two volume, I have got this error:

Volume registration is started in working directory: /var/folders/z8/4grvc78d4nn0d4nhy2l4869w0000gn/T/Slicer/Elastix/20170507_000009_410
Register volumes…
Register volumes using: /Applications/elastix_macosx64_v4.8/bin/elastix: [‘-f’, u’/var/folders/z8/4grvc78d4nn0d4nhy2l4869w0000gn/T/Slicer/Elastix/20170507_000009_410/input/fixed.mha’, ‘-m’, u’/var/folders/z8/4grvc78d4nn0d4nhy2l4869w0000gn/T/Slicer/Elastix/20170507_000009_410/input/moving.mha’, ‘-out’, u’/var/folders/z8/4grvc78d4nn0d4nhy2l4869w0000gn/T/Slicer/Elastix/20170507_000009_410/result-transform’, ‘-p’, ‘/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Resources/RegistrationParameters/Parameters_Rigid.txt’, ‘-p’, ‘/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Resources/RegistrationParameters/Parameters_BSpline.txt’]
‘LD_LIBRARY_PATH’
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Elastix.py”, line 327, in onApplyButton
movingVolumeMaskNode = self.movingVolumeMaskSelector.currentNode())
File “/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Elastix.py”, line 556, in registerVolumes
ep = self.startElastix(inputParamsElastix)
File “/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Elastix.py”, line 466, in startElastix
return subprocess.Popen([executableFilePath] + cmdLineArguments, env=self.getElastixEnv(),
File “/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Elastix.py”, line 433, in getElastixEnv
elastixEnv[“LD_LIBRARY_PATH”] = elastixLibDir + os.pathsep + elastixEnv[“LD_LIBRARY_PATH”]
KeyError: ‘LD_LIBRARY_PATH’

I could not figure this problem out, Any help will be appreciated.
Sincerely
Kaiwei Han M.D.
Department of Neurosurgery, Changzheng Hospital, Shanghai, China.

2

I’ve made the path setup more robust, which hopefully will fix the problem.

To try the fix right now, update “/Applications/Slicer.app/Contents/Extensions-25996/SlicerElastix/lib/Slicer-4.7/qt-scripted-modules/Elastix.py” file on your computer: change elastixEnv["LD_LIBRARY_PATH"]... line to the one shown here: https://github.com/lassoan/SlicerElastix/blob/master/Elastix/Elastix.py#L433

Or, use Slicer’s nightly version that you download tomorrow or later.

1 Like
3

to Andras Lasso，thank you very much，problem solved.