[Neuroimaging] [Dipy] Re: Warnings when running free water model Message-ID:

Rafael Henriques rafaelnh21 at gmail.com
Tue Jan 2 10:58:12 EST 2018


Hi Arnold,

This is just warning you that in some voxel/voxel's the fwDTI's non-linear
convergence procedure did not reach the global minimum with the default
number of iteration defined in scipy.optimize.leastsq. For faster
convergence try using fwDTI's Jacobian by calling the fwDTI model in the
following way:

fwdtimodel = fwdti.FreeWaterTensorModel(grab, fit_method="NLS", jac=True)

This warning is typically generated by background voxels. I also recommend
you to mask your data when fitting.

Best,
Rafael Henriques



> Date: Thu, 28 Dec 2017 22:11:21 -0600
> From: Arnold Evia <ajevia at gmail.com>
> To: neuroimaging at python.org
> Subject: [Neuroimaging] [Dipy] Warnings when running free water model
> Message-ID:
>         <CALqRRQRjHaUqTF16Ayphhq+VrBT25jT5iUZ1M4tZE3R1LENTPQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I am applying the free water dti model to my data, and receive the
> following warnings:
>
> /Users/arnoldevia/anaconda3/lib/python3.6/site-packages/
> scipy/optimize/minpack.py:427:
> RuntimeWarning: Number of calls to function has reached maxfev = 1800.
>   warnings.warn(errors[info][0], RuntimeWarning)
>
> /Users/arnoldevia/personal_programs/dipy/dipy/reconst/fwdti.py:454:
> RuntimeWarning: overflow encountered in exp
>   y = (1-f) * np.exp(np.dot(design_matrix, tensor[:7])) + \
>
> The code I am using is essentially the same as the code used in the free
> water model documentation.
> What do these warnings mean, and what should I do to address them?
> Please let me know if additional information is needed.
>
> Thanks in advance!
> -Arnold Evia
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