<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"><p style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">Hi all, </span><span style="color:black"></span></p><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">I've written a previous email explaining in more detail the process leading up to this epoching issue, but it seems that the email has been hung up waiting for moderator approval. I'll start from the beginning: </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">Here is where I load up the raw data, which was imported from the CMI database in a .raw format:</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">raw=mne.io.read_raw_egi (raw_file_path, montage= mne.channels.read_montage(kind= 'GSM-HydrocCel-129'), preload=True, verbose= True)</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style=""><p style="color:rgb(33,33,33);margin:0px"><br></p><p style="color:rgb(33,33,33);margin:0px"><font face="Arial, sans-serif, serif, EmojiFont">Output: </font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" style="" color="#0000ff">Reading EGI header from [raw_file_path] ....</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" color="#0000ff">Reading events..</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" color="#0000ff">Assembling measurement info...</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" color="#0000ff">Synthesizing trigger channel 'STI 014' ...</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" style="" color="#0000ff">Excluding events {101,102,103.....[etc] } </font><font face="Arial, sans-serif, serif, EmojiFont" style="" color="#000000">(the events listed as being excluded here have the same labels as the nonsense channels talked about below-- not sure what to make of that)</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" style="" color="#0000ff">Reading 0 .... 168248 = 0.000 ... 336.496 secs ....</font></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"> </p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">Upon importing the raw file there are quite a few channels that seem to be not 'real' scalp or external electrodes included in the raw object. One of them, 'STI 014,' is useful for reading the eyes closed/eyes open events but there are about 50 other channels that contain no data and are randomly labeled.</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont"><a href="http://raw.info">raw.info</a>['ch_names'][129:]</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> yields a list of these nonsensical channels: </span><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">[ '101' , '102' , '3' , '11' ,........]</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">I split up and re-concatenate the raw dataset into its respective eyes-open and eyes-closed sections, and proceed from there with 2 sets of raw data.</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">After going through several standard preprocessing steps (filtering, re-referencing, ICA) without a hitch, I run into my issue with epoching the data into 2 seconds.</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">The sample frequency is 500 Hz, so I construct an array of trigger </span><span style="font-family:Arial,sans-serif,serif,EmojiFont"><span style="color:rgb(34,34,34)">events by sampling every 1000th index and appending it to the array with a made-up trigger code of 7. </span></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">print(epoch_array) </span><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">yields</span><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont"> [ [ 0, 0, 7], [1000, 0, 7], [2000, 0, 7], [ 3000, 0, 7].....]</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">I use this array to construct the epoch object:</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">twoSec_epoch = mne.Epochs(eyes_closed_raw, events=epoch_array, tmin=0, tmax=0, event_id={'twoSec':7}, reject=None, flat=None, reject_by_annotation=False)</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><br></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px">Output:</p><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><font color="#0000ff">93 matching events found</font></p><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><font color="#0000ff">Applying baseline correction (mode: mean)</font></p><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><font color="#0000ff">Not setting metadata</font></p><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><font color="#0000ff">0 projection items activated</font></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style=""><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">And of the 93 epochs in twoSec_epoch, the first 28 of them are being dropped seemingly without reason.</span><span style="font-family:Arial,sans-serif,serif,EmojiFont"></span></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont"><br></span></p><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="font-family:Arial,sans-serif,serif,EmojiFont"><font color="#0000ff">twoSec_epoch.get_data()</font></span></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont"><br></span></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">Output:</span><br></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" color="#0000ff">Loading data for 93 events and 1001 original time points ...</font></p><p style="margin:0px"><font face="Arial, sans-serif, serif, EmojiFont" color="#0000ff">28 bad epochs dropped</font></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont"><br></span></p><p style="color:rgb(33,33,33);font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">This happens whether or not the empty channels are dropped from the raw object before creating the epoch object.</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">twoSec_epoch.drop_log[:28]</span><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont"> yields </span><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">[ ['NO_DATA'], ['NO_DATA'], ['NO_DATA'].....]</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:black;font-family:Arial,sans-serif,serif,EmojiFont">But I know that the 'real' electrodes (with the random fake channels dropped) do contain data for these epochs:</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">raw_data_mat= eyes_closed_raw.get_data()</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">first_28_epochs= raw_data_mat[:128, 0:28*1000]</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">print(sum(sum(np.isnan(first_28_epochs)))) </span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:blue;font-family:Arial,sans-serif,serif,EmojiFont">print(sum(sum(first_28_epochs==0)))</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"></span></p></div><div style="font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">yields </span><span style="font-family:Arial,sans-serif,serif,EmojiFont"><font color="#0000ff">0 </font></span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">and </span><span style="font-family:Arial,sans-serif,serif,EmojiFont"><font color="#0000ff">0</font></span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">, ie there is data for each of the 128 channels. </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">I am unsure whether the issue is with the epoch_array I'm making or with something else about this particular dataset. Any help/guesses would be greatly appreciated!</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont"> </span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">Thank you and best wishes,</span></p></div><div style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont"><p style="font-family:Calibri,sans-serif,serif,EmojiFont;margin:0px"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif,serif,EmojiFont">Dillan Cellier</span></p></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Jan 7, 2019 at 10:56 AM Molfese, Peter (NIH/NIMH) [C] <<a href="mailto:peter.molfese@nih.gov">peter.molfese@nih.gov</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 lang="EN-US"><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 class="gmail-m_6148230322631791622WordSection1">
<p class="MsoNormal">Hi Dillan-<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">How are you reading in the data? From the EGI formatted file? Can you provide more of the code?
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman",serif">-- <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman",serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman",serif">Peter J. Molfese, Ph.D. [C] | Scientist, NIMH<br>
Section on Functional Imaging Methods<br>
Building 10, 1D80<br>
10 Center Dr<br>
Bethesda, MD 20892-1148<br>
Email: <a href="mailto:peter.molfese@mail.nih.gov" target="_blank"><span style="color:rgb(5,99,193)">peter.molfese@mail.nih.gov</span></a><br>
Phone: (301) 402-1350<u></u><u></u></span></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Dillan Cellier <<a href="mailto:cellierdillan@gmail.com" target="_blank">cellierdillan@gmail.com</a>><br>
<b>Reply-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>Date: </b>Monday, January 7, 2019 at 11:53 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] epochs with no data?<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><u></u><u></u></p>
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<p class="MsoNormal">Hi Denis, <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Apologies for the delay in getting back to you. I've tried reproducing this with a MNE sample dataset, and did not get the same effect. It would appear then, that there might be something special about the data. Unfortunately this dataset
is not one that I collected. It was acquired from the Child Mind Institute and as such, the extent of my knowledge about it goes only so far as the public information provided on it! <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I tried this on a different subject's data from the same CMI dataset. I got the same results where the epoch.plot() is dropping over half of the epochs, however this time this the drop_log is empty (!?!?!) and at this point i am thoroughly
confused. Here is the code where I am constructing this Epoch object, so that you may see that there shouldn't be any automatic rejection taking place: <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">mne.Epochs(eyes_closed, events=epoch_array, tmin=0, tmax=2, event_id={'twoSec':7}, picks=scalpData, reject_by_annotation=False)<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Any other guesses? Thank you for your help!<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best wishes,<u></u><u></u></p>
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<p class="MsoNormal">Dillan<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Fri, Jan 4, 2019 at 3:30 PM Denis A. Engemann <<a href="mailto:denis-alexander.engemann@inria.fr" target="_blank">denis-alexander.engemann@inria.fr</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hum. That sounds puzzling. Can you reproduce this somehow with the MNE sample data? That could help to see if there is something wrong in the code or if something is special about your data.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
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<p class="MsoNormal">Denis<u></u><u></u></p>
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On 4 Jan 2019, at 22:24, Dillan Cellier <<a href="mailto:cellierdillan@gmail.com" target="_blank">cellierdillan@gmail.com</a>> wrote:<u></u><u></u></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><u></u><u></u></p>
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<p class="MsoNormal">Hi Denis, <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">The events are 2 seconds apart from each other.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thanks!<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Dillan<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Fri, Jan 4, 2019 at 3:18 PM Denis A. Engemann <<a href="mailto:denis-alexander.engemann@inria.fr" target="_blank">denis-alexander.engemann@inria.fr</a>> wrote:<u></u><u></u></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><u></u><u></u></p>
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<p class="MsoNormal">Hi Dillan,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">What is then the distance in seconds between any two events that you passed to the epochs constructor?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Denis<u></u><u></u></p>
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On 4 Jan 2019, at 22:12, Dillan Cellier <<a href="mailto:cellierdillan@gmail.com" target="_blank">cellierdillan@gmail.com</a>> wrote:<u></u><u></u></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><u></u><u></u></p>
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<p class="MsoNormal">Hi Denis, <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I limited the tmin and tmax of the epoch to 0 and 2, respectively, since I don't any kind of stimulus onset in these epochs and don't want them to overlap. This is partly what puzzles me, as I would think this would prevent any inclusion
of not-real data. My resting state data can be cut into 93 two-second time windows, and this the number of events I am feeding into the epoch object. It is labeling 41 of these 93 as 'NO_DATA'. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thank you very much!<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Dillan<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Fri, Jan 4, 2019 at 3:05 PM Denis A. Engemann <<a href="mailto:denis-alexander.engemann@inria.fr" target="_blank">denis-alexander.engemann@inria.fr</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi Dillan,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">This can happen when the epochs selected include (theoretical) samples beyond the (actual) data range. You should not have many of those epochs. Can you roughly tell how many no_data labels you found? I‘d need to refresh my knowledge of
the epochs reading code a bit to see if there may be other reasons for this. Let‘s see what the others say in the meantime.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
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<p class="MsoNormal">Denis<u></u><u></u></p>
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On 4 Jan 2019, at 21:56, Dillan Cellier <<a href="mailto:cellierdillan@gmail.com" target="_blank">cellierdillan@gmail.com</a>> wrote:<u></u><u></u></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><u></u><u></u></p>
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<p class="MsoNormal">Hello again! <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thank you for your responses on my last question, they were very helpful. I am running into another problem now, however. I am epoching resting state data into arbitrary 2 second windows. I am not automatically rejecting epochs by annotation
nor by a rejection parameter. I see that the epoch object's drop_log is recording nearly the whole first half of the epochs as "NO_DATA" epochs, however the raw file contains data for those time indices. I am unsure what could be going on to result in this
loss of data, however it seems especially problematic due to the amount of epochs dropped. Thank you in advance, again!<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best wishes,<u></u><u></u></p>
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<p class="MsoNormal">Dillan<u></u><u></u></p>
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