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Hi all,
I get an error trying to read fif files from Biomag competition into
MNE (https://box.bic.mni.mcgill.ca/s/Biomag2018). The error message is
below. The same file converts fine in Matlab. Any idea?
Thanks,
Vladimir
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`mne show_fiff 226_RAW.fif` had these lines after the measurement info
section:
103 = FIFFB_PROCESSED_DATA
206 = FIFF_COMMENT/FIFF_DESCRIPTION (15b str) = Single
category ... str len=15
104 = FIFFB_EVOKED
...
?
You can read it with `mne.read_evokeds('226_RAW.fif')`. Here is the
`evoked.plot()`:
[image: Figure_1.png]
So these data are stored in evoked format, not raw.
Eric
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Hi all,
I get an error trying to read fif files from Biomag competition into
MNE (https://box.bic.mni.mcgill.ca/s/Biomag2018). The error message is
below. The same file converts fine in Matlab. Any idea?Thanks,
Vladimir
------------------
raw = mne.io.read_raw_fif('226_RAW.fif', preload=True, allow_maxshield
= True, verbose='error')
Traceback (most recent call last):File "<ipython-input-3-c948947cad43>", line 1, in <module>
raw = mne.io.read_raw_fif('226_RAW.fif', preload=True,
allow_maxshield = True, verbose='error')File
"C:\wtcnapps\Anaconda3\envs\mne\lib\site-packages\mne\io\fiff\raw.py",
line 459, in read_raw_fif
preload=preload, verbose=verbose)File "<string>", line 2, in __init__
File "C:\wtcnapps\Anaconda3\envs\mne\lib\site-packages\mne\utils.py",
line 728, in verbose
return function(*args, **kwargs)File
"C:\wtcnapps\Anaconda3\envs\mne\lib\site-packages\mne\io\fiff\raw.py",
line 87, in __init__
preload, do_check_fname)File "<string>", line 2, in _read_raw_file
File "C:\wtcnapps\Anaconda3\envs\mne\lib\site-packages\mne\utils.py",
line 729, in verbose
return function(*args, **kwargs)File
"C:\wtcnapps\Anaconda3\envs\mne\lib\site-packages\mne\io\fiff\raw.py",
line 165, in _read_raw_file
raise ValueError('No raw data in %s' % fname)ValueError: No raw data in D:\Tempdata\Competition\226\226_RAW.fif
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Thanks. That solves it. I now ran into a different issue trying to make a
BEM model. I get the same error for all the 3 subjects (see below). I ran a
sequence of commands as in the documentation and that same sequence worked
for me before on a different example. Please advise.
One thing that might be relevant is that I used the --force option in
make_scalp_surfaces.
Thanks,
Vladimir
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sorry I don't see the error.
btw it must work as we have played with these data successfully.
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Sorry, my mistake. The command and the error are below.
Thanks,
Vladimir
In [117]: bem_file=subject+'-bem.fif'
...:
...: if op.isfile(bem_file):
...: bem = mne.read_bem_surfaces(bem_file)
...: else:
...: bem = mne.make_bem_model(mri_dir)
...: mne.write_bem_surfaces(bem_file, bem)
Creating the BEM geometry...
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
Going from 5th to 4th subdivision of an icosahedron (n_tri: 20480 -> 5120)
outer skin CM is 0.90 -5.99 -0.58 mm
outer skull CM is 0.90 -5.96 -1.02 mm
inner skull CM is 0.85 -6.62 6.36 mm
Checking that outer skull surface is inside outer skin surface...
Checking that inner skull surface is inside outer skull surface...
Traceback (most recent call last):
File "<ipython-input-117-e6e8d7e63470>", line 6, in <module>
bem = mne.make_bem_model(mri_dir)
File "<string>", line 2, in make_bem_model
File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/utils.py",
line 729, in verbose
return function(*args, **kwargs)
File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 572, in make_bem_model
surfaces = _surfaces_to_bem(surfaces, ids, conductivity, ico)
File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 502, in _surfaces_to_bem
_check_surfaces(surfs, incomplete=incomplete)
File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 443, in _check_surfaces
_assert_inside(surf_2, surf_1)
File "/home/vladimir/.conda/envs/mne/lib/python3.6/site-packages/mne/bem.py",
line 432, in _assert_inside
% (_surf_name[fro['id']], _surf_name[to['id']]))
RuntimeError: Surface inner skull is not completely inside surface outer skull
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use :
bem = mne.make_bem_model(mri_dir, conductivity=[0.3])
to use a single layer BEM. it should work.
Alex
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Thanks, that helps. Two more questions:
1) How do I compute covariance? There is a method for raw and epochs
but this data is evoked type.
2) Is it possible to regularise by reducing dimensionality and not use
noise covariance? This is related to the discussion we had with Alex
and others off this list, regarding the best settings for MaxFiltered
data.
Thanks,
Vladimir
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hi,
1) How do I compute covariance? There is a method for raw and epochs
but this data is evoked type.
you could make a RawArray from a bit of the data in the Evoked instance.
or you can use this:
http://martinos.org/mne/stable/generated/mne.make_ad_hoc_cov.html#mne.make_ad_hoc_cov
2) Is it possible to regularise by reducing dimensionality and not use
noise covariance? This is related to the discussion we had with Alex
and others off this list, regarding the best settings for MaxFiltered
data.
where do you want to reduce dimensionality?
Alex
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I want to reduce the dimensionality of the data and the lead-fields
and do beamforming in this reduced space. How would you normally do
beamforming on MaxFiltered data in this case?
I would use empty room data or prestim on which I had run Maxfilter
to get a noise cov and it would go fine.
Would you use the
pre-seizure part to compute noise covariance?
I don't have enough experience to argue here. I don't know
what to do precisely here given the data we have access to.
Alex
