[Mne_analysis] Empty room BTI-to-FIF error

Bear, Joshua JOSHUA.BEAR at ucdenver.edu
Wed Sep 26 13:56:31 EDT 2018
Search archives:

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 <http://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,

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 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180926/109d97ab/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1521 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180926/109d97ab/attachment.bin 
-------------- next part --------------
        External Email - Use Caution        
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180926/109d97ab/attachment-0001.html 

More information about the Mne_analysis mailing list