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daducci / AMICO

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data
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Changing the NODDI parallel diffusivity in AMICO v2.0.0 #188

Closed minisagan closed 3 months ago

minisagan commented 3 months ago

Hi,

I was previously able to update the NODDI parallel diffusivity by editing the models.py script, however, this file is no longer present in lib/python3.9/site-packages/amico after installing v2.0.0.

In a previous issue, it was mentioned that the model parameters could be updated via AMICO.model.set( dPar, ... ), but I am not entirely sure which parameters this will update and want to avoid changing the wrong thing.

How should I proceed?

Kind regards,

Saga

daducci commented 3 months ago

Dear Saga,

No need to modify the core code, you can simply change the model parameters via the set() function of the model itself, something like the following snippet:

ae = amico.Evaluation()
...
...
ae.set_model('NODDI')
dPar = 1.7E-3 # --- THIS IS THE PARALLEL DIFFUSIVITY YOU WANT TO CHANGE ---
dIso  = 3.0E-3
IC_VFs    = np.linspace(0.1,0.99,12)
IC_ODs    = np.hstack((np.array([0.03, 0.06]),np.linspace(0.09,0.99,10)))
isExvivo  = False
ae.model.set(dPar, dIso, IC_VFs, IC_ODs, isExvivo)
ae.generate_kernels(regenerate=True)
...
...

Hope this helps you!