ActiveAx

[zicongzhou818]

Hello,

Thank you for this awesome diffusion MRI integration in python!

I followed the NODDI tutorial and it went very well. But, next, when I tried ActiveAx, I encountered the following error at the step ae.fit() . Would you please help or suggest where to debug? I am not sure why it somehow asking model_name='CylinderZeppelinBall' for an variable 'isExvivo' which is only specified in model_name='NODDI'. I tried re-installation of dmri-amico and this error still popping out.

Best,
Zicong

runfile('/home/.../Documents/ActiveAx_test/sub_01/Example_activeax.py', wdir='/home/.../Documents/ActiveAx_test/sub_01')

-> Precomputing rotation matrices:
[ DONE ]
-> Loading data:
* DWI signal
- dim = 128 x 256 x 3 x 372
- pixdim = 0.400 x 0.400 x 0.500
* Acquisition scheme
- 372 samples, 4 shells
- 12 @ b=0 , 90 @ b=13199.8 , 90 @ b=1926.6 , 90 @ b=1933.3 , 90 @ b=3095.8
* Binary mask
- dim = 128 x 256 x 3
- pixdim = 0.400 x 0.400 x 0.500
- voxels = 338
[ 1.2 seconds ]
-> Preprocessing:
* Normalizing to b0... [ min=0.00, mean=0.79, max=8.46 ]
* Keeping all b0 volume(s)
[ 0.4 seconds ]
-> Creating LUT for "Cylinder-Zeppelin-Ball" model:
[ 1.6 seconds ]
-> Resampling LUT for subject ".":
[ 0.2 seconds ]
-> Estimating principal directions (OLS):
[ 00h 00m 00s ]
-> Fitting 'Cylinder-Zeppelin-Ball' model to 338 voxels (using 96 threads):
Traceback (most recent call last):
File ~/anaconda3/lib/python3.11/site-packages/spyder_kernels/py3compat.py:356 in compat_exec
exec(code, globals, locals)
File ~/Documents/ActiveAx_test/sub_01/Example_activeax.py:22
ae.fit()
File ~/anaconda3/lib/python3.11/site-packages/amico/core.py:466 in fit
results = self.model.fit(self)
File amico/models.pyx:532 in amico.models.CylinderZeppelinBall.fit
File amico/models.pyx:533 in amico.models.CylinderZeppelinBall.fit
File amico/models.pyx:535 in amico.models.CylinderZeppelinBall.fit
File ~/anaconda3/lib/python3.11/concurrent/futures/_base.py:449 in result
return self.__get_result()
File ~/anaconda3/lib/python3.11/concurrent/futures/_base.py:401 in __get_result
raise self._exception
File ~/anaconda3/lib/python3.11/concurrent/futures/thread.py:58 in run
result = self.fn(*self.args, **self.kwargs)
File amico/models.pyx:549 in amico.models.CylinderZeppelinBall._fit
AttributeError: 'CylinderZeppelinBall' object has no attribute 'isExvivo'