Under Ubuntu 20.04, sitkUtils.PullVolumeFromSlicer() works fine in Slicer 5.0.3. In 5.2.1 and later, the call consistently raises an error: File "/bin/slicer5.2.1/Slicer-5.2.1-linux-amd64/bin/Python/sitkUtils.py", line 36, in PullVolumeFromSlicer sitkimage = sitk.ReadImage(myNodeFullITKAddres…

SimpleITK works in Slicer with a customized version. I would be suspicious if any of your additional python packages uninstalled/installed a different version of SimpleITK.

Using Slicer 5.2.1 on Windows I do not observe an error with the following code: import SampleData mrhead_volume = SampleData.SampleDataLogic().downloadMRHead() import sitkUtils as su simpleitk_image = su.PullVolumeFromSlicer(mrhead_volume) There were some fixes for sitkUtils functionality made b…

I am using the official Slicer 5.2.1 download. However, there are a number of additional packages installed into it, some of which are in-house code. Your question prompted me to try a clean download, and the problem does not reproduce. Thank you for that, I will investigate our post-installation st…

One of our in-house dependencies specified a different version of SimpleITK, which replaced Slicer’s custom version, leading to the issue. Thank you for such prompt assistance!

Can you provide us info with which package was changing the SimpleITK version? Was it choosing the a newer or older SimpleITK version? This issue with updating SimpleITK is currently tracked at: Slicer's embedded SimpleITK can be removed by pip …

An in-house package specified SimpleITK==2.1.1 as an install requirement. I believe that is older than the custom 2.2.0 version specified by Slicer. The issue you linked is precisely the one I am facing.

Setting an exact version requirement for a Python package in a complex system is a really bad idea. Dependencies can be so tangled that by setting exact version requirements for a few packages can almost guarantee a failure somewhere. Usually exact version requirement are not even necessary, but it …

Yet another case of a Python package requiring a very specific SimpleITK version has come up - see Run a Python script as subprocess from Slicer - #12 by lassoan @jcfr is there a solution for this? There are a number of bad-behaving Python packages out there that require a certain SimpleITK versio…

Did sitkUtils.PullVolumeFromSlicer() break with Slicer 5.2?

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jamesobutler (James Butler) December 21, 2022, 1:48am 5

Xref the following error which happened upon installing a python package that installed another version of SimpleITK rather than keeping the Slicer customized version.

Topic		Replies	Views
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SimpleITK import error Support	25	4447	March 2, 2021
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Did sitkUtils.PullVolumeFromSlicer() break with Slicer 5.2?

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