[Mne_analysis] error with interpolate_bads

[Sophie Herbst]

Hi Mainak,
after uninstalling all the packages and reinstalling anaconda, the errors
persisted, but now the error messages contained the right path to my
anaconda installation.
I finally found out that there were two apparently independent issues, one
with scipy's cobyla function and one with numpy's einsum function:
https://github.com/scipy/scipy/issues/8118
https://github.com/numpy/numpy/issues/10343
I managed to fix it by manually editing cobyla and uninstalling and
reinstalling numpy (not sure why the updated version wasn't installed right
away).
Not sure whether my solution is the cleanest one, but I thought it might be
usefull to know these issues in case someone else runs into similar
problems.
Best,
Sophie



Mainak Jas <mainakjas at gmail.com> schrieb am Di., 20. Feb. 2018 um 18:21 Uhr:

> Hi Sophie,
>
> I suspect you have conflicting python packages in your
> /home/sh252228/.local/ directory which are installed when you use the flag
> --user with pip. There is a priority order for the packages to be imported
> and it's possible you are importing some library which is not from Anaconda
> or an older version.
>
> Make sure you have removed everything that is in
> site.getusersitepackages() and site.getsitepackages(). Only after that,
> make a fresh install of Anaconda.
>
> I would recommend asking your sysadmin for help if you're still stuck.
>
> Best,
> Mainak
>
>
> On Tue, Feb 20, 2018 at 5:55 PM, Sophie Herbst <ksherbst at googlemail.com>
> wrote:
>
>> Hi Mainak,
>> sorry to bug you again, but it still doesn't work.
>>
>> I uninstalled and reinstalled anaconda following the descriptions on the
>> mne website.
>> When installing the dependencies, I run into this
>> <https://github.com/conda/conda/issues/5985> issue and followed the work
>> around of creating an environment for mayavi.
>> I get no error messages during installation, but still the same errors
>> with interpolate_bads.
>> Any idea what I could do?
>>
>> Thank you!
>> Sophie
>>
>> Sophie Herbst <ksherbst at googlemail.com> schrieb am Di., 20. Feb. 2018 um
>> 17:00 Uhr:
>>
>>> Hi Mainak,
>>> Indeed. It doesn't reproduce on another system.
>>> Thank you for pointing that out!
>>> Sophie
>>>
>>> Mainak Jas <mainakjas at gmail.com> schrieb am Di., 20. Feb. 2018 um
>>> 16:10 Uhr:
>>>
>>>> Hi Sophie,
>>>>
>>>> If I had to guess, I would say you have an installation problem. Can
>>>> you make sure you reproduce this problem on other systems?
>>>>
>>>> Mainak
>>>>
>>>> On Tue, Feb 20, 2018 at 10:56 AM, Sophie Herbst <
>>>> ksherbst at googlemail.com> wrote:
>>>>
>>>>> Dear list,
>>>>> I am running into errors when trying to interpolate bad channels.
>>>>> I have tried it on different versions of my M/EEG data, but the
>>>>> problem is there from the raw import (data recorded at Neurospin). Running
>>>>> interpolate_bads on freshly imported data (no maxfilter applied) gives the
>>>>> errors below. Same after applying Maxfilter (and adding a bad MEG channel).
>>>>>
>>>>> Any help would be greatly appreciated.
>>>>> Best, Sophie
>>>>>
>>>>> *Picking either meg, mag or grad:*
>>>>> File
>>>>> "/home/sh252228/.local/lib/python2.7/site-packages/numpy/core/einsumfunc.py",
>>>>> line 710, in einsum_path
>>>>> "not match previous terms.", char, tnum)
>>>>>
>>>>> ValueError: ("Size of label '%s' for operand %d does not match
>>>>> previous terms.", 'i', 1)
>>>>>
>>>>> *Picking EEG:*
>>>>> File
>>>>> "/home/sh252228/.local/lib/python2.7/site-packages/scipy/optimize/cobyla.py",
>>>>> line 252, in _minimize_cobyla
>>>>> rhoend=rhoend, iprint=iprint, maxfun=maxfun,
>>>>>
>>>>> UnboundLocalError: local variable 'iprint' referenced before assignment
>>>>>
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