[Mne_analysis] Empty room BTI-to-FIF error

[Alexandre Gramfort]

        External Email - Use Caution        

hi Josh,

can you share the empty room data with a script crashes?

thanks
Alex


On Wed, Sep 26, 2018 at 7:57 PM Bear, Joshua <JOSHUA.BEAR at ucdenver.edu> wrote:
>
> Hello everyone,
>
> I’m working with some BTI data and would like to include empty room recordings done prior to the patient recordings for my noise covariance. When importing the data using mne.io.read_raw_bti() I have to set convert=False or I get an error. Then, when trying to save the data to the FIF format, I will get the same error, presumably because it is now trying to perform the conversion function that I had previously avoided.
>
> I do not have any problems with the actual subject recordings, only the empty room one.
>
> I’ve included the error message below. Has anyone seen this before and/or have suggestions on how to get my empty room data converted to FIF?
>
> Thank you for your help,
> Josh
>
>
>
>
> This is the error that appears to occur during BTI to FIF conversion:
>
> Reading 4D PDF file /mystudy/06%29%18 at 13:28/1/c,rfhp0.1Hz...
> Creating Neuromag info structure ...
> ... Setting channel info structure.
> ... putting coil transforms in Neuromag coordinates
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "<string>", line 2, in read_raw_bti
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 729, in verbose
>     return function(*args, **kwargs)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1398, in read_raw_bti
>     eog_ch=eog_ch, preload=preload, verbose=verbose)
>   File "<string>", line 2, in __init__
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/utils.py", line 729, in verbose
>     return function(*args, **kwargs)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1031, in __init__
>     sort_by_ch_name=sort_by_ch_name, eog_ch=eog_ch)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 1209, in _get_bti_info
>     t = _convert_coil_trans(t, dev_ctf_t, bti_dev_t)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/io/bti/bti.py", line 250, in _convert_coil_trans
>     t = combine_transforms(invert_transform(dev_ctf_t), bti_dev_t,
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/mne/transforms.py", line 576, in invert_transform
>     return Transform(trans['to'], trans['from'], linalg.inv(trans['trans']))
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/linalg/basic.py", line 946, in inv
>     a1 = _asarray_validated(a, check_finite=check_finite)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/scipy/_lib/_util.py", line 238, in _asarray_validated
>     a = toarray(a)
>   File "/Users/joshbear/bin/anaconda3/envs/mne/lib/python3.6/site-packages/numpy/lib/function_base.py", line 1233, in asarray_chkfinite
>     "array must not contain infs or NaNs")
> ValueError: array must not contain infs or NaNs
>
>
>
>
>
> Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy
> 13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285
>
>         External Email - Use Caution
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis