<div dir="ltr">Hello Isaiah,<br><div class="gmail_extra"><br><br><div class="gmail_quote">2014-08-29 0:07 GMT+02:00 Isaiah C. Smith <span dir="ltr"><<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu" target="_blank">Isaiah.C.Smith.17@dartmouth.edu</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hello Denis,
<div><br>
</div>
<div>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?</div>
<div>
<pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div><span></span></div></pre></div></div>
</blockquote><div><br></div><div>you mean how to read the matfiles?</div><div><br></div><div>import <a href="http://scipy.io">scipy.io</a></div><div><br></div><div>mat = io.loadmat('mymatfile.mat')</div><div> </div>
<div>but be careful, matfiles are often very nested. It can take while to access everything that's in there.</div><div>It's usually represented as python dictionary and numpy structured array, just to give you some buzz words you can google.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px">
<div><span>sfreq</span> <span style="font-weight:bold">=</span> <span style="color:rgb(0,153,153)">1e3 % sampling rate</span></div><div><br></div></pre></div></div></blockquote><div><br></div><div>yes</div><div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
</div><div><span>ch_types</span> <span style="font-weight:bold">=</span> <span>[</span><span style="color:rgb(221,17,68)">'misc'</span><span>]</span> <span style="font-weight:bold">*</span> <span style="color:rgb(0,153,153)">248 % "248" to “64” channels and ‘misc’ to ‘eeg'</span></div>
<div> </div></pre></div></div></blockquote><div>yes, put 'eeg' here and your channel number.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
<span>ch_names</span> <span style="font-weight:bold">=</span> <span>[</span><span style="color:rgb(221,17,68)">'MISC {:03d}'</span><span style="font-weight:bold">.</span><span>format</span><span>(</span><span>i</span> <span style="font-weight:bold">+</span> <span style="color:rgb(0,153,153)">1</span><span>)</span> <span style="font-weight:bold">for</span> <span>i</span> <span style="font-weight:bold">in</span> <span style="color:rgb(0,134,179)">range</span><span>(</span><span style="color:rgb(0,134,179)">len</span><span>(</span><span>ch_type</span><span>))] % This one I think you can directly copy </span></div>
</pre></div></div></blockquote><div><br></div><div>yes</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
</div><div><span>info</span> <span style="font-weight:bold">=</span> <span>mne</span><span style="font-weight:bold">.</span><span>create_info</span><span>(</span><span>ch_names</span><span style="font-weight:bold">=</span><span>ch_names</span><span>,</span> <span>sfreq</span><span style="font-weight:bold">=</span><span>sfreq</span><span>,</span> <span>ch_types</span><span style="font-weight:bold">=</span><span>ch_types</span><span>) % Directly copy</span></div>
</pre></div></div></blockquote><div><br></div><div>yes </div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
</div><div><span>raw</span> <span style="font-weight:bold">=</span> <span>mne</span><span style="font-weight:bold">.</span><span>io</span><span style="font-weight:bold">.</span><span>RawArray</span><span>(</span><span>data</span><span>,</span> <span>info</span><span>) % data is the a N*M matrix (N is the number of channel, M is the number of timepoints</span></div>
</pre></div></div></blockquote><div><br></div><div>exactly</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
<span style="line-height:16.7999992370605px"><br></span></div><div><span style="line-height:16.7999992370605px">raw</span><span style="line-height:16.7999992370605px;font-weight:bold">.</span><span style="line-height:16.7999992370605px">save</span><span style="line-height:16.7999992370605px">(</span><span style="line-height:16.7999992370605px;color:rgb(221,17,68)">'misc.fif'</span><span style="line-height:16.7999992370605px">) % directly copy</span></div>
<div><span style="line-height:16.7999992370605px"><br></span></div></pre></div></div></blockquote><div><br></div><div>yes, chose an approrpiate name, e.g. 'subject-1-raw.fif'</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><pre style="font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;margin-top:0px;margin-bottom:0px;width:748px;color:rgb(51,51,51);line-height:16.7999992370605px"><div>
<span style="line-height:16.7999992370605px"></span></div><div><br></div></pre>
<div></div>
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<div><cfg.mat></div>
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<div></div>
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<div><data.mat></div>
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<div><elec.mat></div>
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<div><a href="https://drive.google.com/file/d/0B2VQnrnlkkKETl9jUDVtb3JyNlk/edit?usp=sharing" target="_blank">https://drive.google.com/file/d/0B2VQnrnlkkKETl9jUDVtb3JyNlk/edit?usp=sharing</a></div>
<div><a href="https://drive.google.com/file/d/0B2VQnrnlkkKEWEJGT1JpaHd3SW8/edit?usp=sharing" target="_blank">https://drive.google.com/file/d/0B2VQnrnlkkKEWEJGT1JpaHd3SW8/edit?usp=sharing</a></div>
<div><a href="https://drive.google.com/file/d/0B2VQnrnlkkKEWms0S0ozdTgxLTg/edit?usp=sharing" target="_blank">https://drive.google.com/file/d/0B2VQnrnlkkKEWms0S0ozdTgxLTg/edit?usp=sharing</a></div>
<div><br>
</div>
</div>
<div>
<div></div>
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<div>These are the data set that I am working with. Do they correspond? </div>
<div><br></div></div></blockquote><div><br></div><div>what do you mean by 'correspond'? </div><div><br></div><div>basically anything goes as long as you know how to access the actual data arrays.</div><div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div>
</div>
<div>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?</div>
<div><br></div></div></blockquote><div><br></div><div>yes. sounds like it. but you also need to add a montage / the channel positions you might have measured using a polhemus device.</div><div><br></div><div>here's a pull request on that which I abandond. Will be back on this around October.</div>
<div><br></div><div><a href="https://github.com/mne-tools/mne-python/pull/1390">https://github.com/mne-tools/mne-python/pull/1390</a><br></div><div><br></div><div>This code hopefully gives you an idea about what's to do for adding channel posiitons.</div>
<div><br></div><div><a href="https://github.com/dengemann/mne-python/blob/montage/mne/montages/montage.py#L148">https://github.com/dengemann/mne-python/blob/montage/mne/montages/montage.py#L148</a><br></div><div><br></div>
<div><br></div><div>HTH,</div><div>Denis </div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word"><div>
</div>
<div><br>
</div>
<div>Thanks, </div><span class=""><font color="#888888">
<div>Isaiah </div></font></span><div><div class="h5">
<div>
<div>On Aug 25, 2014, at 3:52 PM, Isaiah C. Smith <<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu" target="_blank">Isaiah.C.Smith.17@dartmouth.edu</a>> wrote:</div>
<br>
<blockquote type="cite">
<div style="word-wrap:break-word">
Thanks Denis,
<div><br>
</div>
<div>I will tell you how it goes.</div>
<div><br>
</div>
<div>Isaiah<br>
<div>
<div>On Aug 25, 2014, at 3:47 PM, Denis-Alexander Engemann <<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">Dear Isaiah,
<div><br>
</div>
<div>Here's an example of how to do it:</div>
<div><br>
</div>
<div><a href="https://gist.github.com/dengemann/e9b45f2ff3e3380907d3" target="_blank">https://gist.github.com/dengemann/e9b45f2ff3e3380907d3</a><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">I hope this helps.</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">-Denis<br>
<br>
<div class="gmail_quote">2014-08-26 0:10 GMT+02:00 Denis A. Engemann <span dir="ltr">
<<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi Isaiah,<br>
<br>
yes this is correct.<br>
Take look at the documentation string to get an idea how to use it,<br>
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.<br>
<br>
Please let me know how it goes.<br>
<br>
HTH,<br>
Denis<br>
<div>
<div><br>
<br>
<br>
> On 25 Aug 2014, at 23:53, "Isaiah C. Smith" <<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu" target="_blank">Isaiah.C.Smith.17@dartmouth.edu</a>> wrote:<br>
><br>
> Thanks Denis for the response,<br>
><br>
> 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?<br>
><br>
> Isaiah<br>
><br>
>> On Aug 25, 2014, at 12:19 PM, Denis A. Engemann <<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>> wrote:<br>
>><br>
>> We have mne.io.RawArray, mne.EpochsArray and mne. EvokedArray for such cases.<br>
>> Once you can extract the data and some info on sampling rate it's trivial to construct fiff compatible data-structures..<br>
>> Unfortunately we still don't have an example for that in MNE-Python ...<br>
>><br>
>> --Denis<br>
>><br>
>>> On 25 Aug 2014, at 20:25, <a href="mailto:dgwakeman@gmail.com" target="_blank">dgwakeman@gmail.com</a> wrote:<br>
>>><br>
>>> Hi Isaiah,<br>
>>><br>
>>> 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.<br>
>>><br>
>>> HTH<br>
>>> D<br>
>>><br>
>>> Sent from my phone<br>
>>><br>
>>>> On Aug 25, 2014, at 14:23, "Isaiah C. Smith" <<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu" target="_blank">Isaiah.C.Smith.17@dartmouth.edu</a>> wrote:<br>
>>>><br>
>>>> Hello Experts,<br>
>>>><br>
>>>> 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?<br>
>>>><br>
>>>> These are the formats of the electrode location files that I have.<br>
>>>> <Screen Shot 2014-08-24 at 12.33.11 PM.png><br>
>>>><br>
>>>><br>
>>>> And these are the formats of the EEG data that I have.<br>
>>>><br>
>>>> <Screen Shot 2014-08-24 at 12.33.27 PM.png><br>
>>>><br>
>>>><br>
>>>> Thank you,<br>
>>>> Isaiah Smith<br>
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