Two ITK packages in Slicer

muratmaga · November 10, 2025, 11:40pm

When I try to register two volumes using our ANTsPy extension, I get this error on Linux. Things workout perfectly fine on Windows and Mac:

Switch to module:  "ANTsRegistration"
WARNING: In /project/itksource/Modules/Core/Common/src/itkObjectFactoryBase.cxx, line 543
Possible incompatible factory load:
Running itk version :
itk version 5.4.3
Loaded factory version:
itk version 5.4.4
Loading factory:
/home/maga/Downloads/Slicer-5.10.0-linux-amd64/bin/../lib/Slicer-5.10/ITKFactories/libMRMLIDIOPlugin.so

But when I look at the packages ANTsRegistration is loading, I am not seeing an ITK-5.4.3 being brought in:

[DEBUG][Qt] 10.11.2025 15:23:05 [] (unknown:0) - Switch to module:  "ANTsRegistration"
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting antspyx
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached antspyx-0.6.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.1 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting pandas (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached pandas-2.3.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting pyyaml (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Requirement already satisfied: numpy in ./lib/Python/lib/python3.12/site-packages (from antspyx) (2.0.2)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting statsmodels (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached statsmodels-0.14.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (9.5 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting webcolors (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached webcolors-25.10.0-py3-none-any.whl.metadata (2.2 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting matplotlib (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached matplotlib-3.10.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Requirement already satisfied: Pillow in ./lib/Python/lib/python3.12/site-packages (from antspyx) (11.2.1)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Requirement already satisfied: requests in ./lib/Python/lib/python3.12/site-packages (from antspyx) (2.32.3)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Collecting scikit-learn (from antspyx)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) -   Using cached scikit_learn-1.7.2-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
[INFO][Stream] 10.11.2025 15:23:06 [] (unknown:0) - Requirement already satisfied: scipy<1.16 in ./lib/Python/lib/python3.12/site-packages (from antspyx) (1.13.1)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting contourpy>=1.0.1 (from matplotlib->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached contourpy-1.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting cycler>=0.10 (from matplotlib->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting fonttools>=4.22.0 (from matplotlib->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached fonttools-4.60.1-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (112 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting kiwisolver>=1.3.1 (from matplotlib->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached kiwisolver-1.4.9-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.3 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: packaging>=20.0 in ./lib/Python/lib/python3.12/site-packages (from matplotlib->antspyx) (25.0)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: pyparsing>=3 in ./lib/Python/lib/python3.12/site-packages (from matplotlib->antspyx) (3.2.3)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: python-dateutil>=2.7 in ./lib/Python/lib/python3.12/site-packages (from matplotlib->antspyx) (2.9.0.post0)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: six>=1.5 in ./lib/Python/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib->antspyx) (1.17.0)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting pytz>=2020.1 (from pandas->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting tzdata>=2022.7 (from pandas->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: charset-normalizer<4,>=2 in ./lib/Python/lib/python3.12/site-packages (from requests->antspyx) (3.4.2)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: idna<4,>=2.5 in ./lib/Python/lib/python3.12/site-packages (from requests->antspyx) (3.10)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: urllib3<3,>=1.21.1 in ./lib/Python/lib/python3.12/site-packages (from requests->antspyx) (2.4.0)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Requirement already satisfied: certifi>=2017.4.17 in ./lib/Python/lib/python3.12/site-packages (from requests->antspyx) (2025.4.26)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting joblib>=1.2.0 (from scikit-learn->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting threadpoolctl>=3.1.0 (from scikit-learn->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Collecting patsy>=0.5.6 (from statsmodels->antspyx)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) -   Using cached patsy-1.0.2-py2.py3-none-any.whl.metadata (3.6 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached antspyx-0.6.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (22.4 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached matplotlib-3.10.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.7 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached contourpy-1.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (362 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached fonttools-4.60.1-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (4.9 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached kiwisolver-1.4.9-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.5 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached pandas-2.3.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.4 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (807 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached scikit_learn-1.7.2-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (9.5 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached joblib-1.5.2-py3-none-any.whl (308 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached statsmodels-0.14.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (10.4 MB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached patsy-1.0.2-py2.py3-none-any.whl (233 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Using cached webcolors-25.10.0-py3-none-any.whl (14 kB)
[INFO][Stream] 10.11.2025 15:23:07 [] (unknown:0) - Installing collected packages: pytz, webcolors, tzdata, threadpoolctl, pyyaml, patsy, kiwisolver, joblib, fonttools, cycler, contourpy, scikit-learn, pandas, matplotlib, statsmodels, antspyx
[INFO][Stream] 10.11.2025 15:23:21 [] (unknown:0) -
[INFO][Stream] 10.11.2025 15:23:21 [] (unknown:0) - Successfully installed antspyx-0.6.1 contourpy-1.3.3 cycler-0.12.1 fonttools-4.60.1 joblib-1.5.2 kiwisolver-1.4.9 matplotlib-3.10.7 pandas-2.3.3 patsy-1.0.2 pytz-2025.2 pyyaml-6.0.3 scikit-learn-1.7.2 statsmodels-0.14.5 threadpoolctl-3.6.0 tzdata-2025.2 webcolors-25.10.0

When I try to run pip_uninstall("itk==5.4.3") I get skipping, not installed message. when I check for itk version I get 5.4.4

>>> import itk
>>> itk.__version__
'5.4.4'

It is not clear to me or @dzenanz where this itk-5.4.3 is coming from. Again this is specific to the Linux and is reproducible all recent previews, and today’s stable. Any suggestion is much appreciated.

jamesobutler · November 11, 2025, 2:01am

It appears that AntsPy does not use ITK’s Python package but instead builds ITK C++ from source and uses that along with wrapping it using a package called nanobind.

I observe similar warnings about possible incompatible factory load when I connect an OpenIGTLink connection using PlusToolkit’s PlusServer that uses a slightly different ITK version than the one used by Slicer core and corresponding SlicerOpenIGTLink extension. I observe the warning, but generally don’t face any issues because the versions are similar enough.

Here is the C++ ITK build that uses ITK 5.4.3.

github.com/ANTsX/ANTsPy

scripts/configure_ITK.bat

50bdb2445


      
          SET itkgit=https://github.com/InsightSoftwareConsortium/ITK.git
          :: 5.4.3
          SET itktag=0913f2a962d28eb5725a50a17304c4652ca6cfdc

muratmaga · November 11, 2025, 5:29am

Thanks @jamesobutler

I will try to build a custom wheel using 5.4.4.post1, but don’t know how to get that ITK tag.

Do you know where I can find that information?

Found it: f98d5fac5e1d5ef694f3010f12bbbc2c792994c6

muratmaga · November 11, 2025, 6:28am

Looks like the custom antspyx wheel with itk-5.4.4 seems to solve the crash. I will make changes in SlicerANTsPy to use this custom wheel on Linux. Thanks @jamesobutler

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