[Mne_analysis] Empty room BTI-to-FIF error
Bear, Joshua
JOSHUA.BEAR at ucdenver.edu
Wed Sep 26 15:31:23 EDT 2018
Alex, thank you for the response. I’ve sent another email with files.
Denis, yes, I just checked the empty room recordings for the other subjects in this study as well as a recording I obtained some months ago. I am able to open them in Brainstorm but get the same error across all files in MNE-python. I thought I had previously pulled the older empty room recording into a prior version of MNE-Python, but I can’t remember with certainty.
Cheers,
Josh
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
> On Sep 26, 2018, at 1:25 PM, Denis-Alexander Engemann <denis.engemann at gmail.com> wrote:
>
> External Email - Use Caution
>
>
> Keep me in the loop. I may be able to help. Can you btw. exclude that it is an issue for that particular file?
> On Wed 26 Sep 2018 at 21:02, Alexandre Gramfort <alexandre.gramfort at inria.fr <mailto:alexandre.gramfort at inria.fr>> wrote:
> 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 <mailto: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
> >
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