As the newest version 5.9.0 appeard, I found some new extensions.
One of these is MOOSE extension, but unfortunatelly it doesnt work.
Every time I click install dependencies, I wait even couple hours and nothing happens.
All I can see is:
Would be great if someone can tell me if had the same problem, or solved it, and how 
It would be helpful if you can provide the log file (CTRL + 0). Also what OS are you running? On MacOS with 5.8.0 it seems to install the dependencies fine and starts the segmentation task.
I tried to use it on Windows 11… Is is available only on OS?
No, it is available. but it looks like Moose brings a lot of python packages. If one of them is not available or has issues, it will probaby not going to work. THat’s why you want to look into your log file and see if there are any errors reported.
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Using cached zipp-3.21.0-py3-none-any.whl (9.6 kB)
Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl (6.8 kB)
Downloading future-1.0.0-py3-none-any.whl (491 kB)
Downloading locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Building wheels for collected packages: moosez, acvl-utils, halo, nnunetv2, batchgenerators, batchgeneratorsv2, dynamic-network-architectures
Building wheel for moosez (setup.py): started
Building wheel for moosez (setup.py): finished with status 'done'
Created wheel for moosez: filename=moosez-3.0.6-py3-none-any.whl size=39657 sha256=fbdbde94d706c0186bfb766577970260afc6d7ae35ed0222e0b6e0f65f1f7a22
Stored in directory: /private/var/folders/fj/1nyb9wg10hz1nmtq9kqvskwjt46qsd/T/pip-ephem-wheel-cache-2hwkvaty/wheels/87/92/26/cd3075c30751fa3f01c8d0eff9755f35325c053eb19ecd8e2d
Building wheel for acvl-utils (setup.py): started
Building wheel for acvl-utils (setup.py): finished with status 'done'
Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=f60c2f10be5533fb8f847a858b36f192d8c99732502e39fe7b36f050d6fd86e9
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
Building wheel for halo (setup.py): started
Building wheel for halo (setup.py): finished with status 'done'
Created wheel for halo: filename=halo-0.0.31-py3-none-any.whl size=11232 sha256=0fa82b99f082921174dea203774d2fd7b93a5d5396e82aadcaed3fe88bcec38f
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/bb/85/47/b7c7338ab52808105f937bd8c04aec5d98a543311ac2c8bed2
Building wheel for nnunetv2 (pyproject.toml): started
Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
Created wheel for nnunetv2: filename=nnunetv2-2.5.1-py3-none-any.whl size=264369 sha256=317ef6e69d7c89cfb82f10b47b01c34342b32fe43998f8051a3feb11c9671266
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/7b/85/af/51e5381b7cf9cc417ca071b9cd6e35afc59236a0ebb4462249
Building wheel for batchgenerators (setup.py): started
Building wheel for batchgenerators (setup.py): finished with status 'done'
Created wheel for batchgenerators: filename=batchgenerators-0.25.1-py3-none-any.whl size=93093 sha256=e00d7cacba78345a19aa659b2fc33e37cc53eff7322b315fe6bba67e4bcb1daf
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/97/8d/b9/3a9435d619b6a4bcd98f8cb8b324da29b6173555bb80860bdd
Building wheel for batchgeneratorsv2 (pyproject.toml): started
Building wheel for batchgeneratorsv2 (pyproject.toml): finished with status 'done'
Created wheel for batchgeneratorsv2: filename=batchgeneratorsv2-0.2.1-py3-none-any.whl size=45187 sha256=e68e69a34705856d48dbf19313c670b48399a3ac19a948dcae4ea01e33044980
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/8c/29/14/3fdf4a97638724355746fb142b55db6868f1c0f1698af26ebd
Building wheel for dynamic-network-architectures (setup.py): started
Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30051 sha256=3e434889e376b36ee09e485f2f0ef207dca923a10b4f386bedd37df295c2a1c7
Stored in directory: /Users/amaga/Library/Caches/pip/wheels/ec/59/c1/e65ad8b5ac7df95651f913251875b4cc8275644e0e28e82c63
Successfully built moosez acvl-utils halo nnunetv2 batchgenerators batchgeneratorsv2 dynamic-network-architectures
Installing collected packages: spinners, pyfiglet, linecache2, argparse, zipp, traceback2, tqdm, toolz, tifffile, termcolor, pyyaml, python-gdcm, pygments, pydicom, psutil, natsort, mdurl, locket, lazy-loader, kiwisolver, imageio, imagecodecs, graphviz, future, fonttools, et-xmlfile, einops, cycler, contourpy, connected-components-3d, colorama, cloudpickle, click, yacs, unittest2, scikit-image, partd, openpyxl, mpire, markdown-it-py, log_symbols, importlib-resources, importlib-metadata, rich, nibabel, matplotlib, halo, fft-conv-pytorch, dynamic-network-architectures, dask, batchgenerators, seaborn, dicom2nifti, batchgeneratorsv2, acvl-utils, nnunetv2, moosez
Attempting uninstall: pydicom
Found existing installation: pydicom 2.4.4
Uninstalling pydicom-2.4.4:
Successfully uninstalled pydicom-2.4.4
Successfully installed acvl-utils-0.2 argparse-1.4.0 batchgenerators-0.25.1 batchgeneratorsv2-0.2.1 click-8.1.8 cloudpickle-3.1.1 colorama-0.4.6 connected-components-3d-3.22.0 contourpy-1.3.0 cycler-0.12.1 dask-2024.8.0 dicom2nifti-2.4.11 dynamic-network-architectures-0.3.1 einops-0.8.0 et-xmlfile-2.0.0 fft-conv-pytorch-1.2.0 fonttools-4.55.7 future-1.0.0 graphviz-0.20.3 halo-0.0.31 imagecodecs-2024.12.30 imageio-2.37.0 importlib-metadata-8.6.1 importlib-resources-6.5.2 kiwisolver-1.4.7 lazy-loader-0.4 linecache2-1.0.0 locket-1.0.0 log_symbols-0.0.14 markdown-it-py-3.0.0 matplotlib-3.9.4 mdurl-0.1.2 moosez-3.0.6 mpire-2.3.5 natsort-8.1.0 nibabel-5.3.2 nnunetv2-2.5.1 openpyxl-3.0.10 partd-1.4.2 psutil-6.1.1 pydicom-2.2.2 pyfiglet-0.8.post1 pygments-2.19.1 python-gdcm-3.0.24.1 pyyaml-6.0.2 rich-13.9.4 scikit-image-0.24.0 seaborn-0.13.2 spinners-0.0.24 termcolor-2.5.0 tifffile-2024.8.30 toolz-1.0.0 tqdm-4.67.1 traceback2-1.4.0 unittest2-1.1.0 yacs-0.1.8 zipp-3.21.0
Okey! Thanks, here it is
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Session start time …: 20250129_165911
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Slicer version …: 5.9.0-2025-01-26 (revision 33428 / 2a19ce0) win-amd64 - installed release
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Operating system …: Windows / Professional / (Build 26100, Code Page 65001) - 64-bit
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Memory …: 65460 MB physical, 69556 MB virtual
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - CPU …: AuthenticAMD AMD Ryzen 7 5700X 8-Core Processor , 16 cores, 16 logical processors
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Application path …: C:/Users/Bartek/AppData/Local/slicer.org/Slicer 5.9.0-2025-01-26/bin
[DEBUG][Qt] 29.01.2025 16:59:11 (unknown:0) - Additional module paths …: slicer.org/Extensions-33428/AirwaySegmentation/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/AirwaySegmentation/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/TotalSegmentator/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/TissueSegmentation/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SurfaceWrapSolidify/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SurfaceFragmentsRegistration/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerVMTK/lib/Slicer-5.9/qt-loadable-modules, slicer.org/Extensions-33428/SlicerVMTK/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerPythonTestRunner/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerDevelopmentToolbox/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerDentalModelSeg/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/SlicerDentalModelSeg/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerConda/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SkullStripper/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/AutomatedDentalTools/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/AutomatedDentalTools/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/BrainVolumeRefinement/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/CurveMaker/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/DCMQI/lib/Slicer-5.9/cli-modules, slicer.org/Extensions-33428/DebuggingTools/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/DentalSegmentator/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/ExtraMarkups/lib/Slicer-5.9/qt-loadable-modules, slicer.org/Extensions-33428/HDBrainExtraction/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/MONAIAuto3DSeg/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/MONAILabel/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/MONAIViz/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/MarkupsToModel/lib/Slicer-5.9/qt-loadable-modules, slicer.org/Extensions-33428/NNUNet/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/PyTorch/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/QuantitativeReporting/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/Sandbox/lib/Slicer-5.9/qt-loadable-modules, slicer.org/Extensions-33428/Sandbox/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SegmentEditorExtraEffects/lib/Slicer-5.9/qt-loadable-modules, slicer.org/Extensions-33428/SegmentEditorExtraEffects/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SegmentationVerification/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerMOOSE/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SegmentHumanBody/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/RVXLiverSegmentation/lib/Slicer-5.9/qt-scripted-modules, slicer.org/Extensions-33428/SlicerElastix/lib/Slicer-5.9/qt-scripted-modules
[CRITICAL][Qt] 29.01.2025 16:59:14 (unknown:0) - Error(s):
CLI executable: C:/Users/Bartek/AppData/Local/slicer.org/Slicer 5.9.0-2025-01-26/slicer.org/Extensions-33428/SlicerVMTK/lib/Slicer-5.9/qt-loadable-modules/vtkvmtk.py
The process failed to start. Either the invoked program is missing, or you may have insufficient permissions to invoke the program.
[CRITICAL][Qt] 29.01.2025 16:59:14 (unknown:0) - Fail to instantiate module “vtkvmtk”
[CRITICAL][Qt] 29.01.2025 16:59:14 (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 29.01.2025 16:59:14 (unknown:0) - vtkvmtk
[DEBUG][Python] 29.01.2025 16:59:14 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Slicer-5.9\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 29.01.2025 16:59:14 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Slicer-5.9\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 29.01.2025 16:59:15 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Python] 29.01.2025 16:59:15 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Slicer-5.9\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: Elastix
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib_init_.py:341) - matplotlib data path: C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib\mpl-data
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib_init_.py:341) - CONFIGDIR=C:\Users\Bartek.matplotlib
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib_init_.py:1512) - interactive is False
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib_init_.py:1513) - platform is win32
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib_init_.py:341) - CACHEDIR=C:\Users\Bartek.matplotlib
[DEBUG][Python] 29.01.2025 16:59:17 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\lib\Python\Lib\site-packages\matplotlib\font_manager.py:1580) - Using fontManager instance from C:\Users\Bartek.matplotlib\fontlist-v390.json
[DEBUG][Qt] 29.01.2025 16:59:24 (unknown:0) - Switch to module: “MOOSE”
[INFO][Python] 29.01.2025 16:59:26 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\slicer.org\Extensions-33428\PyTorch\lib\Slicer-5.9\qt-scripted-modules\PyTorchUtils.py:153) - Importing torch…
[INFO][Python] 29.01.2025 16:59:26 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\slicer.org\Extensions-33428\PyTorch\lib\Slicer-5.9\qt-scripted-modules\PyTorchUtils.py:190) - PyTorch 2.5.1+cu124 imported successfully
[INFO][Python] 29.01.2025 16:59:26 [Python] (C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\slicer.org\Extensions-33428\PyTorch\lib\Slicer-5.9\qt-scripted-modules\PyTorchUtils.py:191) - CUDA available: True
[INFO][Stream] 29.01.2025 16:59:26 (unknown:0) - Collecting git+https://github.com/Keyn34/MOOSE.git@SlicerMOOSE
[INFO][Stream] 29.01.2025 16:59:26 (unknown:0) - Cloning GitHub - Keyn34/MOOSE: MOOSE (Multi-organ objective segmentation) a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research.The pipeline is based on nn-UNet and has the capability to segment 120 unique tissue classes from a whole-body 18F-FDG PET/CT image. (to revision SlicerMOOSE) to c:\users\bartek\appdata\local\temp\pip-req-build-2cq_jshj
[INFO][Stream] 29.01.2025 16:59:26 (unknown:0) -
[INFO][Stream] 29.01.2025 16:59:26 (unknown:0) - ERROR: Cannot find command ‘git’ - do you have ‘git’ installed and in your PATH?
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - File “C:/Users/Bartek/AppData/Local/slicer.org/Slicer 5.9.0-2025-01-26/slicer.org/Extensions-33428/SlicerMOOSE/lib/Slicer-5.9/qt-scripted-modules/MOOSE.py”, line 117, in button_install_dependencies_clicked
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - slicer.util.pip_install(“git+https://github.com/Keyn34/MOOSE.git@SlicerMOOSE”)
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - File “C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\bin\Python\slicer\util.py”, line 3942, in pip_install
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - _executePythonModule(“pip”, args)
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - File “C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\bin\Python\slicer\util.py”, line 3896, in _executePythonModule
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - logProcessOutput(proc)
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - File “C:\Users\Bartek\AppData\Local\slicer.org\Slicer 5.9.0-2025-01-26\bin\Python\slicer\util.py”, line 3862, in logProcessOutput
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
[CRITICAL][Stream] 29.01.2025 16:59:27 (unknown:0) - subprocess.CalledProcessError: Command ‘[‘C:/Users/Bartek/AppData/Local/slicer.org/Slicer 5.9.0-2025-01-26/bin/…/bin\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’, ‘git+https://github.com/Keyn34/MOOSE.git@SlicerMOOSE’]’ returned non-zero exit status 1.
I’ve reported the issue to the SlicerMOOSE developers. You can track the work at:
I’ll track the topic till they’ll find the solution. Thank you very much!