[Mne_analysis] Empty room BTI-to-FIF error

Alexandre Gramfort alexandre.gramfort at inria.fr
Thu Sep 27 08:53:14 EDT 2018
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hi Josh,

we can replicate the problem with Denis. For some reason your config file
has a transform matrix (dev_ctf_t) that contains NaN:

 bti_info['bti_transform'][0]
array([[ 1.        ,  0.        ,  0.        ,         nan],
      [-0.        ,  0.70710678,  0.70710678,         nan],
      [ 0.        , -0.70710678,  0.70710678,         nan],
      [ 1.        ,  1.        ,  1.        ,  1.        ]])

this pops up when reading the bytes from your config file. You can
also use the follow
lines to debug:

------
from mne.io.bti.read import read_char, read_uint32, read_transform, read_float
from mne.io.bti.read import read_int16, read_str, read_int32


with open('config', 'rb') as fid:

    cfg = dict()
    cfg['hdr'] = {'version': read_int16(fid),
                  'site_name': read_str(fid, 32),
                  'dap_hostname': read_str(fid, 16),
                  'sys_type': read_int16(fid),
                  'sys_options': read_int32(fid),
                  'supply_freq': read_int16(fid),
                  'total_chans': read_int16(fid),
                  'system_fixed_gain': read_float(fid),
                  'volts_per_bit': read_float(fid),
                  'total_sensors': read_int16(fid),
                  'total_user_blocks': read_int16(fid),
                  'next_der_chan_no': read_int16(fid)}

    fid.seek(2, 1)
    cfg['checksum'] = read_uint32(fid)
    cfg['reserved'] = read_char(fid, 32)
    cfg['transforms'] = [read_transform(fid) for t in
                         range(cfg['hdr']['total_sensors'])]
    print(cfg['transforms'])
------

I don't know enough about BTi system to have a clue of how to fix this
besides hacking the reader to replace NaNs by zeros.

Alex
On Wed, Sep 26, 2018 at 9:31 PM Bear, Joshua <JOSHUA.BEAR at ucdenver.edu> wrote:
>
> 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> 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> 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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>> > Mne_analysis at nmr.mgh.harvard.edu
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>>
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