Hello Isaiah,
2014-08-29 0:07 GMT+02:00 Isaiah C. Smith <Isaiah.C.Smith.17 at dartmouth.edu>:
Hello Denis,
I am trying to use the python that you posted to Github, and I have a
few questions concerning the parameters. Am I correct in my assumptions
below? And where do I place the file strings to be read?
you mean how to read the matfiles?
import scipy.io
mat = io.loadmat('mymatfile.mat')
but be careful, matfiles are often very nested. It can take while to access
everything that's in there.
It's usually represented as python dictionary and numpy structured array,
just to give you some buzz words you can google.
sfreq = 1e3 % sampling rate
yes
ch_types = ['misc'] * 248 % "248" to ?64? channels and ?misc? to ?eeg'
yes, put 'eeg' here and your channel number.
ch_names = ['MISC {:03d}'.format(i + 1) for i in range(len(ch_type))] % This one I think you can directly copy
yes
info = mne.create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types) % Directly copy
yes
raw = mne.io.RawArray(data, info) % data is the a N*M matrix (N is the number of channel, M is the number of timepoints
exactly
raw.save('misc.fif') % directly copy
yes, chose an approrpiate name, e.g. 'subject-1-raw.fif'
<cfg.mat>
<data.mat>
<elec.mat>
https://drive.google.com/file/d/0B2VQnrnlkkKETl9jUDVtb3JyNlk/edit?usp=sharing
https://drive.google.com/file/d/0B2VQnrnlkkKEWEJGT1JpaHd3SW8/edit?usp=sharing
https://drive.google.com/file/d/0B2VQnrnlkkKEWms0S0ozdTgxLTg/edit?usp=sharing
These are the data set that I am working with. Do they correspond?
what do you mean by 'correspond'?
basically anything goes as long as you know how to access the actual data
arrays.
Sorry, I have been trying to do this for while. Once the data is
changed, I can get the forward model and the gain matrix since I already
have the bems?
yes. sounds like it. but you also need to add a montage / the channel
positions you might have measured using a polhemus device.
here's a pull request on that which I abandond. Will be back on this around
October.
https://github.com/mne-tools/mne-python/pull/1390
This code hopefully gives you an idea about what's to do for adding channel
posiitons.
https://github.com/dengemann/mne-python/blob/montage/mne/montages/montage.py#L148
HTH,
Denis
Thanks,
Isaiah
Thanks Denis,
I will tell you how it goes.
Isaiah
Dear Isaiah,
Here's an example of how to do it:
https://gist.github.com/dengemann/e9b45f2ff3e3380907d3
I hope this helps.
-Denis
2014-08-26 0:10 GMT+02:00 Denis A. Engemann <denis.engemann at gmail.com>:
Hi Isaiah,
yes this is correct.
Take look at the documentation string to get an idea how to use it,
basically you pass the data matrix, the sampling rate, a list of channel
types, like ['eeg'] * 128 for 128 EEG channels and that's it for
constructing a Raw object whose .save method you can then use to create a
fiff file.
Please let me know how it goes.
HTH,
Denis
>
> Thanks Denis for the response,
>
> Do you mean that we can use Evoked Array to Convert the data into the
.fiff? We are able to extract the EEG data & electrode location data
information using matlab. Also, we know the sampling rate information. So
can we use some tools (e.g. mne.io.RawArray, mne.EpochsArray and mne) to
convert into fiff format?
>
> Isaiah
>
>>
>> We have mne.io.RawArray, mne.EpochsArray and mne. EvokedArray for such
cases.
>> Once you can extract the data and some info on sampling rate it's
trivial to construct fiff compatible data-structures..
>> Unfortunately we still don't have an example for that in MNE-Python ...
>>
>> --Denis
>>
>>>
>>> Hi Isaiah,
>>>
>>> You provided the suffixes of the files not the name of the file
types. The first thin I would try to do is look for a file converter or
reader. If you cannot find a converter for whatever file types these are,
but you are able to read the files with some toolbox: you could read in
those data files and replace all of the fields in the raw sample data set
with your data. This is something I only recommend for advanced users as
there are a lot of details you need to keep track of.
>>>
>>> HTH
>>> D
>>>
>>> Sent from my phone
>>>
>>>>
>>>> Hello Experts,
>>>>
>>>> I need to get the gain matrix using MNE. I have made my bem models,
but I need help with the EEG conversion data. Could someone help me through
this process so that I can view the matrix?
>>>>
>>>> These are the formats of the electrode location files that I have.
>>>> <Screen Shot 2014-08-24 at 12.33.11 PM.png>
>>>>
>>>>
>>>> And these are the formats of the EEG data that I have.
>>>>
>>>> <Screen Shot 2014-08-24 at 12.33.27 PM.png>
>>>>
>>>>
>>>> Thank you,
>>>> Isaiah Smith
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