[Neuroimaging] failure using DIPY Free Water Elimination DTI

[Ariel Rokem]

Hi Ping,

I can't quite reproduce your error, though I am getting similar errors.
Could you also share the code that you are running?

For the time being, the one thing that I noticed is that there are NaNs in
your data. That might be causing this issue.

Cheers,

Ariel



On Mon, Dec 31, 2018 at 5:43 AM Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> Hi Ariel,
>
>  Have you got the chance to look at the DWI data that was attached to the
> previous email?
>
> Thank you for your time.
>
> Ping
>
> On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi Ping,
>>
>> Thanks for your email. Hard to say exactly what is going on without
>> further information. Could you tell us more about the data you are using?
>> How many b-values? How many directions? Any chance you could share the data
>> from the voxel that caused that error to be raised?
>>
>> Thanks!
>>
>> Ariel
>>
>> On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh <pinghongyeh at gmail.com>
>> wrote:
>>
>>> Hi Dipy Users,
>>>
>>>  I've ran into errors "Eigenvalues did not  converge" when using the
>>> free water elimination model,
>>> and here is the error message:
>>>
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>> line 1615, in _decompose_tensor_nan
>>>     min_diffusivity=min_diffusivity)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py",
>>> line 1946, in decompose_tensor
>>>     eigenvals, eigenvecs = eigh(tensor)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py",
>>> line 128, in eigh
>>>     return np.linalg.eigh(a, UPLO)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>> line 1291, in eigh
>>>     w, vt = gufunc(a, signature=signature, extobj=extobj)
>>>   File
>>> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py",
>>> line 95, in _raise_linalgerror_eigenvalues_nonconvergence
>>>     raise LinAlgError("Eigenvalues did not converge")
>>> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge
>>>
>>>
>>> Any suggestions?
>>>
>>> Thank you.
>>>
>>> Ping
>>>
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