Empty room BTI-to-FIF error

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1

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,
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

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2

External Email - Use Caution

hi Josh,

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

thanks
Alex

3

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?

4

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

        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?
        External Email - Use Caution

hi Josh,

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

thanks
Alex

>
> 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 <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

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5

External Email - Use Caution

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:

6

Hi Alex,

Thank you for looking into this!

I also don?t know why BTI does that but could ask our MEG physicist. I wonder if it is linked to the head shape information and, since this had no subject, it uses nans to show that.

Would it be relatively trivial to hack the reader? My FieldTrip workaround is effective but a bit clunky and cumbersome, and it would be great to keep everything in python.

Thanks,
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

       External Email - Use Caution

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

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

       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?

       External Email - Use Caution

hi Josh,

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

thanks
Alex

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

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

       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

_______________________________________________
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Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

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7

External Email - Use Caution

If this is a standard output of the BTi system (for example if all your
empty-room recordis are thsi way) and we can figure out the correct way to
deal with it, then yes it shouldn't be too difficult to fix the reader to
deal with this case.

Eric

8

Hi Eric and Alex,

I heard back from Eugene Kronberg, our MEG physicist, who confirmed that this transformation matrix will contain nans with any empty room recordings (unless you chose to record with the head frame system in place despite the absence of a head, I suppose). I?ve attached his response below.

Regards,
Josh

Hi Josh,

Well, the empty room is an empty room, there is no patient and there is no head frame system of coordinates. Transformation matrix in the config file is for rotation and translation between sensor frame and head frame system of coordinates. That's why there are nan(s) in the transformation.

The right thing would be not to use transformation matrix for the empty room recordings. Otherwise, you could try to replace nan(s) with something else.

Good luck,
Eugene

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

If this is a standard output of the BTi system (for example if all your empty-room recordis are thsi way) and we can figure out the correct way to deal with it, then yes it shouldn't be too difficult to fix the reader to deal with this case.

Eric

Hi Alex,

Thank you for looking into this!

I also don?t know why BTI does that but could ask our MEG physicist. I wonder if it is linked to the head shape information and, since this had no subject, it uses nans to show that.

Would it be relatively trivial to hack the reader? My FieldTrip workaround is effective but a bit clunky and cumbersome, and it would be great to keep everything in python.

Thanks,
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

       External Email - Use Caution

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

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

       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?

       External Email - Use Caution

hi Josh,

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

thanks
Alex

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

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9

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Ok that?s what I predicted. Good to have it confirmed. For other BTI data
that we have dealt with it was not an issue as those must have been
recorded with some patient id or so as we do not see nans there. I guess we
can just look for nans and replace them.

Denis

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Hi Josh,

take a look at this PR: https://github.com/mne-tools/mne-python/pull/5566

It fixes the reading of your files for me.

Best,
Denis