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AMYPAD / AmyPET

Amyloid imaging to prevent Alzheimer's Disease
https://amypad.eu
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amypet centiloid requires `MATLAB` #24

Open jhuguetn opened 2 years ago

jhuguetn commented 2 years ago

Running amypad centiloid CLI subcommand fails unless MATLAB platform is found in the current environment/system. See below,

(amypet) user@host:/# amypet centiloid --glob-MRI *.nii.gz --glob-PET *.nii.gz --outfile results.csv /data/mri /data/pet /data/roi/Centiloid_Std_VOI/nifti/2mm
WARNING:miutil.mlab:Python could not find the MATLAB engine.
Attempting to install automatically.
Traceback (most recent call last):
  File "/root/venvs/amypet/lib/python3.7/site-packages/miutil/mlab/__init__.py", line 63, in get_engine
    from matlab import engine
ModuleNotFoundError: No module named 'matlab'

What is exactly required for running AmyPET, full MATLAB environment or the compiler runtime (MCR) is good enough? Additionally, which versions of MATLAB does AmyPET support/require? Any specific toolboxes?

I would add some details on this regard in the README file.

casperdcl commented 2 years ago

yes the underlying packages/dependencies have more info in their READMEs, but we need this info bubbled up/unified in the docs.

Unfortunately MCR isn't (yet) supported - a full MATLAB installation is required. MATLAB versions tend to only work with specific versions of Python so they must match. Specifically, check that your Python version appears in grep supported_version /usr/local/MATLAB/*/extern/engines/python/setup.py.