[Mne_analysis] Maxwell Filter and Projections

[Sam Zorowitz]

@ Dan: We were trying to move away from the command line version for a
number of reasons. As far as I know, there is no -skip option in the python
implementation.

@ Eric: We are using the Anaconda distribution, and I was not able to
reproduce the error from the thread you linked. When we are getting an
error, it looks like this:

RuntimeWarning: invalid value encountered in greater
>   num = np.sum(s > tol, dtype=int)
>


Traceback (most recent call last):
>   File "motion_correction.py", line 32, in <module>
>     raw = maxwell_filter(raw, st_duration=st_duration,
> destination=trans.mean(axis=0), bad_condition='warning')
>
> File "<string>", line 2, in maxwell_filter
>
>  File "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/utils.py",
> line 551, in verbose
>     return function(*args, **kwargs)
>
>  File
> "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/preprocessing/maxwell.py",
> line 404, in maxwell_filter
>     t_proj = _overlap_projector(orig_in_data, resid, st_correlation)
>
>  File
> "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/preprocessing/maxwell.py",
> line 1237, in _overlap_projector
>     overwrite_a=True, mode='economic', **check_disable)[0].T
>
>  File
> "/homes/5/szoro/.local/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py",
> line 142, in qr
>     overwrite_a=overwrite_a)
>
>  File
> "/homes/5/szoro/.local/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py",
> line 20, in safecall
>     ret = f(*args, **kwargs)
>


ValueError: failed to create intent(cache|hide)|optional array-- must have
> defined dimensions but got (0,)


 Unfortunately I can't quite parse what's going on here in the error
message.

On Fri, Mar 25, 2016 at 1:47 PM, Eric Larson <larson.eric.d at gmail.com>
wrote:

> The short of it is that we were running into some issues with the Maxwell
>> filter function, such that the SVD will not converge for certain buffers if
>> there is an abundance of noise.
>>
>
> I have observed seen this "failure to converge" problem with SVD before.
> Are you running Anaconda? If so, could you look here, see if you can
> reproduce the error with the .npy file from the post, and also do the `cat
> /proc/cpuinfo` step? It will help isolate the problem, and keep attention
> on it:
>
> https://github.com/ContinuumIO/anaconda-issues/issues/695
>
> If you're not on Anaconda, I'm curious what Python setup you're using.
>
> Such "high noise" segments really shouldn't be a problem for SVD. If the
> Anaconda folks don't fix the issue, we're going to try to put a workaround
> solution in upstream scipy:
>
> https://github.com/scipy/scipy/pull/5994#issuecomment-200341678
>
> Eric
>
>
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