Add Slicer_ASLtoolkit extension

[acsenrafilho]

New extension

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[acsenrafilho]

@lassoan could you please evaluate this PR as well?

[lassoan]

There is no CLI modules, so you cannot ask the user about installing a Python package. It is OK to install without asking, like this:

try:
    from asltk.asldata import ASLData
    from asltk.reconstruction import CBFMapping
    from asltk.utils import load_image, save_image
except ModuleNotFoundError:
    import slicer.util
    slicer.util.pip_install("asltk")
    from asltk.asldata import ASLData
    from asltk.reconstruction import CBFMapping
    from asltk.utils import load_image, save_image

I could not try to actually use any of the modules, because I could not find any tutorial with testing data.

[acsenrafilho]

Great, @lassoan
Thanks for the advice. I did not know that, for extensions without CLI, it is ok to install the python package directly.
I have changed the code lines in the main branch
Link to ASL sample

BTW, I have also added a small data test zip file here to assist with a (brief) testing.
I will also add this example test data to the documentation, which will be publicly available to users and developers.

[acsenrafilho]

@lassoan , just to say that I have updated the extension documentation to give a quick dataset tutorial to assist for further testing.
See more details in the section Quick tutorial in the documentation

I already included the How to install section assuming that (soon) this extension will be live at Slicer Extension Manager (finger crossed 🤞 )

I hope that this will be useful for the general community. Any thoughts are very welcome!

BTW, thank you very much for all the help!

[lassoan]

Thank you for your patience. Have you tried if slicer.util.messageBox actually works in Python CLI modules? I would expect it to fail. It is because that GUI CLI modules are not meant to provide any interactivity or GUI (other than the GUI that is automatically generated from the .xml file). If there is any message that you want to display to the user then print it to the standard output or standard error. If there is an error then exit with a non-zero exit code.

[acsenrafilho]

Hi @lassoan

Thank you for the suggestion. I made the change in the print messages, using the direct standard output. All the slicer.util.messagebox and similar methods were replaced to be print out as usual.

Is there anything else to be adjusted?

Thank you again for all the tips!

[acsenrafilho]

Hi @jcfr

I am wondering if it is needed to ajust more details in the PR.
Is it ok to be merged?

Please tell me what are the further adjustments to be done (if there is any).

Thank you!

[lassoan]

It should be good, only the extension name and category needs some attention.

❌ Check extension name failed: extension name should not start with 'Slicer'. Please, consider changing it to '_ASLtoolkit'.

Could you update the project name in the top-level CMakeLists.txt file to be ASLToolkit (or maybe ASLtoolkit)? It is good to have the Slicer prefix in the repository name, but not in the extension's name.

❌ Check category failed: Category Arterial Sping Labelling is unknown. Consider using any of the known extensions instead: Active Learning, Analysis, Auto3dgm, BigImage, Cardiac, Chest Imaging Platform, Conda, Converters, DICOM, DSCI, Developer Tools, Diffusion, Examples, Exporter, FTV Segmentation, Filtering, Filtering.Morphology, Filtering.Vesselness, Holographic Display, IGT, Informatics, Netstim, Neuroimaging, Nuclear Medicine, Orthodontics, Osteotomy Planning, Otolaryngology, Photogrammetry, Pipelines, Planning, Printing, Quantification, Radiotherapy, Registration, Remote, Rendering, SPHARM, Segmentation, Sequences, Shape Analysis, Shape Regression, Shape Visualization, Simulation, SlicerCMF, SlicerMorph, Spectral Imaging, Supervisely, Surface Models, SurfaceLearner, Tomographic Reconstruction, Tracking, Tractography, Training, Ultrasound, Utilities, Vascular Modeling Toolkit, Virtual Reality, VisSimTools, Web System Tools, Wizards

Would any of these existing categories work for your extension?

[acsenrafilho]

It should be good, only the extension name and category needs some attention.

❌ Check extension name failed: extension name should not start with 'Slicer'. Please, consider changing it to '_ASLtoolkit'.

Could you update the project name in the top-level CMakeLists.txt file to be ASLToolkit (or maybe ASLtoolkit)? It is good to have the Slicer prefix in the repository name, but not in the extension's name.

❌ Check category failed: Category Arterial Sping Labelling is unknown. Consider using any of the known extensions instead: Active Learning, Analysis, Auto3dgm, BigImage, Cardiac, Chest Imaging Platform, Conda, Converters, DICOM, DSCI, Developer Tools, Diffusion, Examples, Exporter, FTV Segmentation, Filtering, Filtering.Morphology, Filtering.Vesselness, Holographic Display, IGT, Informatics, Netstim, Neuroimaging, Nuclear Medicine, Orthodontics, Osteotomy Planning, Otolaryngology, Photogrammetry, Pipelines, Planning, Printing, Quantification, Radiotherapy, Registration, Remote, Rendering, SPHARM, Segmentation, Sequences, Shape Analysis, Shape Regression, Shape Visualization, Simulation, SlicerCMF, SlicerMorph, Spectral Imaging, Supervisely, Surface Models, SurfaceLearner, Tomographic Reconstruction, Tracking, Tractography, Training, Ultrasound, Utilities, Vascular Modeling Toolkit, Virtual Reality, VisSimTools, Web System Tools, Wizards

Would any of these existing categories work for your extension?

Hi @lassoan

Great, I will make the change in the extension name to remove the Slicer prefix. No problem.

However, regarding the Arterial Sping Labelling category, this still a doubt to me. Is it possible to us to create a new category to ASL (Arterial Sping Labelling) topic? In the list provided in Slicer at the moment, this category is not availble and (in my point of view) it could be nice to include this new topic in MRI analysis (as Diffusion that is already present). What do you think about it?
Anyway, if it is not able to create a new category for ASL, I think that it could fit into the Analysis or Neuroimaging.
What would be appropriate?

Thank you again for the revision in the PR and all the help!

[lassoan]

In the long term we should probably switch to using multiple "tags" to filter and categorize extensions. But for now, to make the single "category" field useful, we need categories that contain more than a few extensions, but not dozens.

How many extensions could go into the "Arterial Spin Labeling" category?

[acsenrafilho]

I see and agree with you @lassoan.
At the moment, I am making the initial development for Slicer in the field of ASL processing. But, maybe in the future, new research groups can enroll to Slicer community and try to add new extension in this area (but it is unclear to me how far this would go...)

In any case, considering that it is in the Slicer planning to add a multiple tag in the future, I could place an exisiting category now and then update it in the future.

If this is good to go, I can make the adjsutment in the code here.

Thanks!

[acsenrafilho]

Hi, @lassoan

I have made the changes in the extension name and category and CI have checked successfuly.

Is anything else needed ?

Thank you again for the support

[lassoan]

Thank you, everything looks good!

Just a few things to consider:

1. I've tried the test data provided at the link and it resulted in computation errors:

No module named 'logic'
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Using cached patsy-1.0.1-py2.py3-none-any.whl (232 kB)
Downloading acres-0.5.0-py3-none-any.whl (12 kB)
Installing collected packages: SimpleITK, docopt, webcolors, universal-pathlib, pygments, patsy, num2words, mdurl, interface-meta, greenlet, dill, click, astor, sqlalchemy, markdown-it-py, kagglehub, acres, statsmodels, rich, formulaic, bidsschematools, bids-validator, antspyx, pybids, asltk
  Attempting uninstall: SimpleITK
    Found existing installation: SimpleITK 2.4.0rc2.dev213
    Uninstalling SimpleITK-2.4.0rc2.dev213:
      Successfully uninstalled SimpleITK-2.4.0rc2.dev213
Successfully installed SimpleITK-2.5.2 acres-0.5.0 antspyx-0.5.4 asltk-0.7.1 astor-0.8.1 bids-validator-1.14.7.post0 bidsschematools-1.1.0 click-8.1.8 dill-0.3.9 docopt-0.6.2 formulaic-0.5.2 greenlet-3.2.4 interface-meta-1.3.0 kagglehub-0.3.13 markdown-it-py-3.0.0 mdurl-0.1.2 num2words-0.5.14 patsy-1.0.1 pybids-0.17.2 pygments-2.19.2 rich-13.9.4 sqlalchemy-2.0.43 statsmodels-0.14.5 universal-pathlib-0.2.6 webcolors-24.11.1
[
    'C:/D/Slicer-ASLtoolkit/CBF_ATT_ASL/CBF_ATT_ASL.py',
    '--outputFolder',
    'C:/tmp/20250918-asltest/output',
    '--inputASL',
    'C:/tmp/20250918-asltest/pcasl.nii.gz',
    '--inputM0',
    'C:/tmp/20250918-asltest/m0_mean.nii.gz',
    '--brainMask',
    'C:/tmp/20250918-asltest/m0_bet_mask.nii.gz',
    '170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0',
    '100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0',
    'C:/Users/andra/AppData/Local/Temp/Slicer/ECGBG_vtkMRMLScalarVolumeNodeB.nr
rd',
    'true',
    'C:/Users/andra/AppData/Local/Temp/Slicer/ECGBG_vtkMRMLScalarVolumeNodeC.nr
rd',
    'false'
]
 --- CBF/ATT ASL Input Data ---
ASL file path: C:/tmp/20250918-asltest/pcasl.nii.gz
ASL image dimension: (8, 7, 17, 80, 80)
Mask file path: C:/tmp/20250918-asltest/m0_bet_mask.nii.gz
Mask image dimension: (17, 80, 80)
M0 file path: C:/tmp/20250918-asltest/m0_mean.nii.gz
M0 image dimension: (17, 80, 80)
PLD: [170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0]
LD: [100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0]
---- Advanced Options ----
Output normalized CBF: True
Average M0: True


2025-09-18 09:16:31 - asltk.asldata - INFO - Creating ASLData object
2025-09-18 09:16:31 - asltk.asldata - INFO - Loading ASL image from: C:/tmp/20250918-asltest/pcasl.nii.gz
2025-09-18 09:16:31 - asltk - INFO - Loaded ASL image: shape=(8, 7, 17, 80, 80), path=C:/tmp/20250918-asltest/pcasl.nii.gz
2025-09-18 09:16:31 - asltk.asldata - INFO - Loading M0 image from: C:/tmp/20250918-asltest/m0_mean.nii.gz
2025-09-18 09:16:31 - asltk - INFO - Loaded M0 image: shape=(17, 80, 80), path=C:/tmp/20250918-asltest/m0_mean.nii.gz
2025-09-18 09:16:31 - asltk.asldata - INFO - ASL timing parameters - LD: [100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0], PLD: [170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0]
2025-09-18 09:16:31 - asltk.cbf_mapping - INFO - Setting brain mask with label 1
Traceback (most recent call last):
  File "C:\D\Slicer-ASLtoolkit\CBF_ATT_ASL\CBF_ATT_ASL.py", line 146, in <module>
    executeScript(args)
  File "C:\D\Slicer-ASLtoolkit\CBF_ATT_ASL\CBF_ATT_ASL.py", line 91, in executeScript
    recon.set_brain_mask(mask_img)
  File "C:\tmp\Slicer 5.8.1\lib\Python\Lib\site-packages\asltk\reconstruction\cbf_mapping.py", line 126, in set_brain_mask
    _check_mask_values(brain_mask, label, self._asl_data('m0').shape)
  File "C:\tmp\Slicer 5.8.1\lib\Python\Lib\site-packages\asltk\aux_methods.py", line 34, in _check_mask_values
    raise TypeError(
TypeError: Image mask dimension does not match with input 3D volume. Mask shape (17, 80, 80) not equal to (80, 80)

2. It could be more convenient to get all the inputs from the scene. Then the user could just drag-and-drop the files to the application window and then in the module select nodes from a dropdown menu. You can keep the file inputs as well, but I would put them in an "Advanced" section, collapsed by default. You could also consider adding te values to the GUI.

3. If you used NRRD format for image storage, you could keep all additional imaging parameters (pld, ld, te) in the image files.