Groupwise registration about simpleelastix HOT 12 CLOSED

It seems JoinSeriesImageFilter does not have support for 4D images at all. This is a bug. Will fix it.

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Hi gattia, JoinSeriesImageFilter should now have support for 4D images. Run git pull in the SimpleElastix source directory and rebuild. Let me know how it goes.

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Thanks for the fix! That did the trick to running the JoinSeries.

Though, I ended up having issues using it because the images have different origins and slightly different axes. Is this common? I got around it by relaxing the tolerances using these commands:
sitk.ProcessObject.SetGlobalDefaultDirectionTolerance(1)
sitk.ProcessObject.SetGlobalDefaultCoordinateTolerance(1)

I also had to set all of the origins to the same as one of the images. I am assuming these changes aren't best practice? Your example doesn't talk about any of these problems but with using any group for MRI or other data I am assuming it would be the case. What is typical practice?

Thanks,

Anthony.

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It is certainly not best practice but I do it myself all the time. I believe the issue is with the origin and direction being slightly modified as they pass through the ITK pipeline, see e.g. this discussion on the ITK mailing list. You may also have to do it after elastix registration (I know I do). I usually just

resultImage.CopyInformation(fixedImage)

because the result image is being transformed to the fixed image domain so these should be equal anyway. The documentation could indeed be improved in this area. You are very welcome to submit a PR, otherwise I will do it when I get the time.

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Thanks for the response. I will take an attempt at a pull request/edit to that portion of the document. It will be my first :).

Anthony.

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Hi !

I built SimpleElastix with the latest git version. Nonetheless I experience exactly the same issue that gattia exposed in his first message.
I hope that you will be able to help me,

Pierre

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Did you set the SimpleITK_4D_IMAGES CMake variable to ON?

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Yes I did.

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What is the error message you are seeing?

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I got the following error for any pixel type :
Traceback (most recent call last): File "dose_tracking_pierre_2.py", line 36, in <module> image = sitk.JoinSeries(image_vector) File "/usr/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 39910, in JoinSeries return _SimpleITK.JoinSeries(*args) RuntimeError: Exception thrown in SimpleITK JoinSeries: /home/pgranger/Documents/Stage_M1/SimpleElastix/Code/Common/include/sitkMemberFunctionFactory.hxx:196: sitk::ERROR: Pixel type: 32-bit signed integer is not supported in 3D byN3itk6simple21JoinSeriesImageFilterE

I just load 3D images and try to Join them in a 4D image.

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Try to pull and rebuild the develop branch and let me know how it goes.

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I did as you said and it perfectly solved my issue, thank you very much !

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