<div dir="ltr">Great, please hop on GitHub and open an mne-python issue, and we'll figure out how to go from there.<div><br></div><div>Cheers,</div><div>Eric</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 9:14 AM, JohnMark Taylor <span dir="ltr"><<a href="mailto:johnmark.taylor@yale.edu" target="_blank">johnmark.taylor@yale.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Yes, using python is definitely an option. Thanks so much for your help :]<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 12:12 PM, Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hey JohnMark,<div><br></div><div>It looks like the events end up being coded incorrectly as tiny fractional numbers (see attched image). From Python I loaded both the converted FIF and the EDF file directly and neither seemed to work properly:</div><div><br></div><div><div>>>> import mne<br></div><div>>>> raw = mne.io.Raw('tb9226_postlearning_withquestions.fif')<br></div><div>>>> mne.find_events(raw, 'Status')<br></div><div>Trigger channel contains negative values. Taking absolute value.</div><div>array([], shape=(0, 3), dtype=int32)</div><div>>>> raw.ch_names</div><div>['FP1', 'FPZ', 'FP2', 'AF3', 'AF4', 'F7', 'F5', 'F3', 'F1', 'FZ', 'F2', 'F4', 'F6', 'F8', 'FT7', 'FC5', 'FC3', 'FC1', 'FCZ', 'FC2', 'FC4', 'FC6', 'FT8', 'T7', 'C5', 'C3', 'C1', 'CZ', 'C2', 'C4', 'C6', 'T8', 'M1', 'TP7', 'CP5', 'CP3', 'CP1', 'CPZ', 'CP2', 'CP4', 'CP6', 'TP8', 'M2', 'P7', 'P5', 'P3', 'P1', 'PZ', 'P2', 'P4', 'P6', 'P8', 'PO7', 'PO5', 'PO3', 'POZ', 'PO4', 'PO6', 'PO8', 'CB1', 'O1', 'OZ', 'O2', 'CB2', 'HEO', 'VEO', 'EMG', 'EKG', 'Status']</div><div>>>> import matplotlib.pyplot as plt<br></div><div>>>> plt.ion()</div><div>>>> plt.plot(raw[-1, :][0].T)<br></div><div>[<matplotlib.lines.Line2D object at 0x7f687b2b7050>]</div><div><br></div><div>>>> raw2 = mne.io.read_raw_edf('tb9226_postlearning_withquestions.edf')</div><div>>>> raw2.ch_names</div><div>[u'FP1', u'FPZ', u'FP2', u'AF3', u'AF4', u'F7', u'F5', u'F3', u'F1', u'FZ', u'F2', u'F4', u'F6', u'F8', u'FT7', u'FC5', u'FC3', u'FC1', u'FCZ', u'FC2', u'FC4', u'FC6', u'FT8', u'T7', u'C5', u'C3', u'C1', u'CZ', u'C2', u'C4', u'C6', u'T8', u'M1', u'TP7', u'CP5', u'CP3', u'CP1', u'CPZ', u'CP2', u'CP4', u'CP6', u'TP8', u'M2', u'P7', u'P5', u'P3', u'P1', u'PZ', u'P2', u'P4', u'P6', u'P8', u'PO7', u'PO5', u'PO3', u'POZ', u'PO4', u'PO6', u'PO8', u'CB1', u'O1', u'OZ', u'O2', u'CB2', u'HEO', u'VEO', u'EMG', u'EKG', 'STI 014']</div><div>>>> raw2[-1, :]</div><div>(array([[ 0., 0., 0., ..., 0., 0., 0.]]), array([ 0.00000000e+00, 2.00000000e-03, 4.00000000e-03, ...,</div><div> 9.10994000e+02, 9.10996000e+02, 9.10998000e+02]))</div><div>>>> raw2[-1, :][0]</div><div>array([[ 0., 0., 0., ..., 0., 0., 0.]])</div><div>>>> plt.plot(raw2[-1, :][0].T)</div><div>[<matplotlib.lines.Line2D object at 0x7f687ab8d490>]</div><div><br></div></div><div>I have a couple ideas of how we could potentially fix this in mne-python related to the channel scaling. Is using Python an option for you?</div><span><font color="#888888"><div><br></div><div>Eric</div></font></span><div><div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 8:49 AM, JohnMark Taylor <span dir="ltr"><<a href="mailto:johnmark.taylor@yale.edu" target="_blank">johnmark.taylor@yale.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Eric, thanks so much for the fast response! Here is a link containing both the pre-conversion .edf file and the post-conversion .fif for a single run of data:<br><br><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_sh_fxvzjuwe0uh2qds_AADAL6-5FrBDlTE3c9gEMkPakLa-3Fdl-3D0&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=XA_8UaiIzSl0pmthQ3yyGTqtStEA3ETHFfIawY99UuQ&m=0myZWd2WmuOCgSwn-PxuPYhQCuZh53j-rqe3pmnMhZ8&s=bfD_Y8nptRlDb1YBThLviytHzPZKcePp5ceMpKe1_5I&e=" target="_blank"><font color="red"><b>MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be</b></font> https://www.dropbox.com/sh/fxvzjuwe0uh2qds/AADAL6_rBDlTE3c9gEMkPakLa?dl=0</a><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 5, 2015 at 11:42 AM, Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hey JohnMark,<div><br></div><div>Could you share small sample versions (preferably a few seconds with some triggers) of the .cnt/.edf/.fif files on dropbox or something? It would help with debugging, unless someone knows the answer offhand. It could be a channel naming issue, or it could be a conversion issue.</div><div><br></div><div>Eric</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Tue, May 5, 2015 at 8:38 AM, JohnMark Taylor <span dir="ltr"><<a href="mailto:johnmark.taylor@yale.edu" target="_blank">johnmark.taylor@yale.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div><div>Hello,<br><br></div>I was wondering if someone could help me with a problem I've been having. We are trying to apply the pipeline described in the Cookbook (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__martinos.org_mne_stable_manual_cookbook.html&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=XA_8UaiIzSl0pmthQ3yyGTqtStEA3ETHFfIawY99UuQ&m=VKj9K7x4U6CliuuAACZi74vjQHCC-viVi2CplD1JjmM&s=7iTVqPuimIC1lYBV4FbLswCejvxNY1FAeg20Z3DkWtw&e=" target="_blank"><font color="red"><b>MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be</b></font> http://martinos.org/mne/stable/manual/cookbook.html</a>) to some EEG data that was collected in the .cnt format (Neuroscan). To convert this data to the .fif format, we are first converting it to an EEGLab .set file, which is converted to a .edf, which we are trying to convert to a .fif file. All of the data makes it through alright, with the exception of the stimulus codes. The stimulus codes <b>do</b> make it to the .edf stage, where they are represented in the channel labeled "status" as skinny spikes whose height corresponds to the value of the stimulus codes (in .cnt and .set formats, they are represented as numerical codes from 0 to 255). Here's the problem: when we then try to convert the .edf files to the .fif format using mne_edf2fif, the stimulus codes seem to get lost in transit (when we try to view the .fif file using mne_browse_raw, it doesn't find any events). <br><br></div>Does anyone know the fix for this? We've tried adding the option "--digtrig status" to mne_browse_raw so it knows where to look for the codes, but this doesn't seem to help anything. I noticed the "tal" and "annotmap" options in mne_ed2fiff, but these seem to apply to edf+ files, not edf files. I have no experience with the edf or fif formats, so there's a possibility I'm just misunderstanding something.<br><br></div>Thanks in advance for any help,<br></div><div><br></div>JohnMark Taylor<br></div>Yale Human Neuroscience Lab<br></div>
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