[Mne_analysis] compute_proj_raw raised 'LinAlgError - SVD did not converge'

[Eric Larson]

There shouldn't be any NaNs in the data (and I thought scipy/numpy checked
for this anyway), so I'd be surprised if it were the same issue. If you're
feeling adventurous you could do "import pdb; pdb.pm()" and then use pdb
commands to debug the issue a little bit. Given that this will probably
required a bit of back-and-forth, I'd suggest opening an mne-python issue
so we can interact without burdening the mne-analysis listserv.

Eric


On Tue, Nov 18, 2014 at 11:15 AM, Dan Howarth <d.c.howarth at gmail.com> wrote:

> I should also note that I do not get this problem with the file if I try
> to do the projection before I band pass and notch filter. Could band
> passing and notch filtering before performing the computation result in a
> situation in which the 'weight matrix' (I have no idea what that is
> reffering to in this context) has negatives?
>
> On Tue, Nov 18, 2014 at 2:13 PM, Dan Howarth <d.c.howarth at gmail.com>
> wrote:
>
>> I tried using Anaconda but that didn't work out either.
>>
>> I found something interesting here:
>> http://stackoverflow.com/questions/23533144/numpy-linalg-linalg-linalgerror-svd-did-not-converge
>>
>> Would it be possible that the 'weights' are negative?
>>
>> On Tue, Nov 18, 2014 at 11:34 AM, Eric Larson <larson.eric.d at gmail.com>
>> wrote:
>>
>>> Unfortunately this is likely due to a bug in LAPACK:
>>>
>>> https://github.com/scipy/scipy/issues/3868
>>>
>>> You could try updating LAPACK, using `python-scipy` and `python-numpy`
>>> from the Ubuntu repos, or possibly using Anaconda instead of the system
>>> Python. Although it's ugly, it also works sometimes to just tweak the
>>> inputs a tiny (seemingly trivial) amount, e.g. by including/excluding one
>>> extra time point or epoch in calculations.
>>>
>>> Eric
>>>
>>>
>>> On Tue, Nov 18, 2014 at 8:18 AM, Dan Howarth <d.c.howarth at gmail.com>
>>> wrote:
>>>
>>>> In our lab we take a 'empty room' recording in which we turn on the MEG
>>>> scanner when no one is in the room in order to further characterize the
>>>> noise.
>>>>
>>>> I haven't had a problem in the past with this function, but for some
>>>> reason its not working for some subjects and working for others.
>>>>
>>>> Here's the pipeline of the data:
>>>>
>>>> max filter -> band pass 1-150 > notch filter 60, 120 > then I compute
>>>> the proj
>>>>
>>>> Python was installed on my ubuntu machine. I use virtualenv
>>>>
>>>> I used pip to install everything.
>>>>
>>>> scipy: 0.14.0
>>>> numpy: 1.9.1
>>>>
>>>> On Tue, Nov 18, 2014 at 3:21 AM, Alexandre Gramfort <
>>>> alexandre.gramfort at telecom-paristech.fr> wrote:
>>>>
>>>>> hi Dan,
>>>>>
>>>>> on what data did you apply this function?
>>>>>
>>>>> how did you install python+numpy+scipy?
>>>>>
>>>>> Alex
>>>>>
>>>>>
>>>>> On Tue, Nov 18, 2014 at 12:26 AM, Dan Howarth <d.c.howarth at gmail.com>
>>>>> wrote:
>>>>> > Hello all,
>>>>> >
>>>>> > I am attempting to use compute_proj_raw
>>>>> > (
>>>>> http://martinos.org/mne/stable/generated/mne.compute_proj_raw.html?highlight=compute_proj_raw#mne.compute_proj_raw
>>>>> )
>>>>> >
>>>>> > However, when I run the program I get the following error:
>>>>> > https://gist.github.com/howarth/ae6289878337cb30af84
>>>>> >
>>>>> > This is from the stable version of mnepython using 'pip install mne'
>>>>> which
>>>>> > was done a few weeks ago.
>>>>> >
>>>>> > Thanks!
>>>>> > Dan Howarth
>>>>> >
>>>>> >
>>>>> >
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