<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr">The error is trying to tell you that the type(events) is not an ndarray, but rather a tuple. If you print(type(events)), you should see "tuple". This is because events_from_annotations returns two values:<div><br></div><div><a href="https://mne.tools/stable/generated/mne.events_from_annotations.html">https://mne.tools/stable/generated/mne.events_from_annotations.html</a><br></div><div><br></div><div>And those two values really come in a tuple. So you need:</div><div><br></div><div>events, event_ids_annot = mne.events_from_annotations(...)</div><div><br></div><div>or something like that. For more information, see:</div><div><br></div><div><a href="https://mne.tools/stable/auto_tutorials/intro/plot_20_events_from_raw.html#converting-between-events-arrays-and-annotations-objects">https://mne.tools/stable/auto_tutorials/intro/plot_20_events_from_raw.html#converting-between-events-arrays-and-annotations-objects</a><br></div><div><br></div><div>Eric</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 23, 2020 at 8:15 PM Daniel Cabral <<a href="mailto:dac0069@auburn.edu">dac0069@auburn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
Hi,</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
Thanks for the response. It worked perfectly. I do have one more question though.</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
I have been struggling to find the events from my files. Here is what I've got so far:</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
I am attaching a vhdr file with the markers</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
import mne<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
mne.set_log_level('WARNING')
<div style="margin:0px">fname = "go.nogo.01.vhdr"</div>
raw = mne.io.read_raw_brainvision(fname, preload=True)<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
montage = mne.channels.make_standard_montage('standard_1020')raw.set_montage(montage, raise_if_subset = False)<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
ica = mne.preprocessing.ICA(n_components=15, random_state=97)
<div style="margin:0px">ica.fit(raw.copy().filter(1,40))</div>
ica.plot_sources(raw);<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
ica.plot_components()<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
raw = ica.apply(raw.copy(), exclude = ica.exclude)
<div style="margin:0px"><br>
</div>
raw.plot();<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
events = mne.events_from_annotations(raw, event_id='auto')
<div style="margin:0px">events;</div>
tmin, tmax = -0.2, 0.5<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
events_nogo_sed = [88,89,90,91,92,93,94,95,96,97,98,99,100,
<div style="margin:0px"> 101,102,103,104,105,106,107,108,109,110,</div>
<div style="margin:0px"> 111,112,113]</div>
<br>
epochs = mne.Epochs(raw, events, events_nogo_sed, tmin, tmax)</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<br>
</div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:black;background-color:rgb(255,255,255)">
<pre style="font-size:14px;font-family:monospace;text-align:left;background-color:white;display:block;border-radius:0px;margin:0px;padding:1px 0px;word-break:break-all;overflow:auto;box-sizing:border-box;white-space:pre-wrap"><span style="margin:0px;font-weight:bold;color:rgb(178,43,49);box-sizing:border-box">TypeError</span>: events should be a NumPy array of integers, got <class 'tuple'></pre>
<br>
</div>
<div style="margin:0px">
<div style="margin:0px"></div>
<div style="margin:0px;font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;color:rgb(0,0,0)">
<br style="font-size:16px;background-color:rgb(255,255,255)">
</div>
</div>
<div>
<div id="gmail-m_-5911877429245688722appendonsend"></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-5911877429245688722divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> on behalf of Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>><br>
<b>Sent:</b> Monday, September 21, 2020 7:05 AM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software <<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>><br>
<b>Subject:</b> Re: [Mne_analysis] No digitization found - ICA</font>
<div> </div>
</div>
<div>
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p>
<p></p>
<div dir="ltr">Your channels appear to use the 10-20 system. Something like this should work:
<div><br>
</div>
<div>import mne<br>
</div>
<div>fname = "go.nogo.01.vhdr"<br>
raw = mne.io.read_raw_brainvision(fname, preload=True)<br>
raw.filter(1, 40)<br>
montage = mne.channels.make_standard_montage('standard_1020')<br>
raw.set_montage(montage, on_missing='ignore') # RIghtEar missing<br>
ica = mne.preprocessing.ICA(n_components=15, random_state=97)<br>
ica.fit(raw)<br>
ica.plot_sources(raw)<br>
ica.plot_components()<br>
</div>
<div><br>
</div>
<div>See for more information:</div>
<div><br>
</div>
<div><a href="https://mne.tools/dev/auto_tutorials/intro/plot_40_sensor_locations.html?highlight=set_montage" target="_blank">https://mne.tools/dev/auto_tutorials/intro/plot_40_sensor_locations.html?highlight=set_montage</a><br>
</div>
<div><br>
</div>
<div>Eric</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Sep 21, 2020 at 8:37 AM Daniel Cabral <<a href="mailto:dac0069@auburn.edu" target="_blank">dac0069@auburn.edu</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p>
<p></p>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hi, </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I am trying to work with a .vhdr file from brainvision. I loaded the data, and did some plots. Then, I tried the ICA, but I ended up with the following error: "No digitization points found". I'm guessing this is related to the set montage. I did a lot of searching,
and I noticed a lot of people have the same issue. Still, I can't seem to find a way to solve this. I am also attaching the file, in case you need. For now, I just want to be able to run the ICA and to properly do the set the montage (if needed). <span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">I
looked all over the MNE website for solutions, but I simply can't work this out.</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">PS: MNE is amazing!</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Here is what I've got so far:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
import mne
<div><br>
</div>
<div>mne.set_log_level('WARNING')</div>
<div>fname = "go.nogo.01.vhdr"</div>
<div>raw = mne.io.read_raw_brainvision(fname, preload=True)</div>
<div><br>
</div>
<div>raw.plot_psd(fmax = 50)</div>
<div><br>
</div>
<div>raw.plot()</div>
<div><br>
</div>
<div>raw.filter(1,40)</div>
<div><br>
</div>
<div>raw.plot()</div>
<div><br>
</div>
<div>raw_new_ref = mne.add_reference_channels(raw, ref_channels=['RightEar'])</div>
<div>raw_new_ref.plot()</div>
<div><br>
</div>
<div>ica = mne.preprocessing.ICA(n_components=15, random_state=97)</div>
<div>ica.fit(raw)</div>
<div>ica.plot_sources(raw)</div>
<div><br>
</div>
<div>ica.plot_components()</div>
<br>
<br>
</div>
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div id="gmail-m_-5911877429245688722x_gmail-m_7024625711199201036Signature">
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b>Daniel Cabral.</b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
PhD student</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Graduate Teaching Assistant</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Performance and Exercise Psychophysiology lab</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
School of Kinesiology</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Auburn University</div>
</div>
</div>
</div>
</div>
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