[Mne_analysis] Maxwell Filter and Projections

Sam Zorowitz szorowi1 at gmail.com
Fri Mar 25 14:28:06 EDT 2016
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@ Dan: Ahh, we were wondering how the -skip function worked. (We looked
through the manual but did not specify.)

@ Eric: Absolutely will do.

All of which brings me back to the original question: Does anyone know a
reason why one shouldn't apply projections before Maxwell filtering?

On Fri, Mar 25, 2016 at 2:22 PM, Eric Larson <larson.eric.d at gmail.com>
wrote:

> That error is different from the SVD one, but I suspect it has the same
> underlying cause (Anaconda using outdated build tools). To avoid derailing
> the original topic too much, can you open an mne-python issue for this
> specific error scipy.linalg error? We can tackle debugging steps there. If
> you can anonymize the file, upload it somewhere, give the minimal steps to
> reproduce it, and paste the output of `mne.sys_info()` (assuming you're on
> `master`) that would help.
>
> Eric
>
>
> On Fri, Mar 25, 2016 at 2:18 PM, Sam Zorowitz <szorowi1 at gmail.com> wrote:
>
>> @ 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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