<div dir="ltr">Couldn't you just modify the epoch data in place? E.g.:<div><br></div><div><div style="font-size:12.8000001907349px">epochs = mne.read_epochs(FILENAME)</div><div style="font-size:12.8000001907349px">epochs._data[:, picks, :] = mne.baseline.rescale(epochs._data[:, picks, :], times=epochs.times, (None, 0), ...)</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">etc?</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Chris</div><blockquote style="font-size:12.8000001907349px;margin:0px 0px 0px 40px;border:none;padding:0px"><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><br></blockquote></blockquote></blockquote></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 10, 2015 at 7:03 PM, David I Leitman <span dir="ltr"><<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">super thanks- dave<div><div class="h5"><br><div><div>On Jul 10, 2015, at 1:02 PM, Teon Brooks <<a href="mailto:teon.brooks@gmail.com" target="_blank">teon.brooks@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">Hi Dave,<div><br></div><div>It would look something like this:</div><div><br></div><div>epochs = mne.read_epochs(FILENAME)</div><div>epochs_bl = mne.EpochsArray(data=epochs.get_data(), info=<a href="http://epochs.info/" target="_blank">epochs.info</a>,</div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">events=epochs.events, tmin=epochs.tmin, event_id=epochs.event_id, baseline=(None, 0))</blockquote></blockquote></blockquote><div><br></div>where (None, 0) is from the beginning of epoch to 0 like Chris mentioned.<br><br><div>and sorry, yes, I meant you can raise an issue on github: <a href="https://github.com/mne-tools/mne-python/issues/new" target="_blank">https://github.com/mne-tools/mne-python/issues/new</a></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr">-teon</div></div></div>
<br><div class="gmail_quote">On Fri, Jul 10, 2015 at 12:47 PM, David I Leitman <span dir="ltr"><<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">HI Teon and chris,<div><br></div><div><div><br></div><div>how do i "pass it to EpochsArray where you can specify a baseline" </div><div><br></div><div>also by raise the issue on mne-pthon -do you mean on github?</div><div><br></div><div>thanks for the help </div><div>dave<div><div><br><div><div>On Jul 10, 2015, at 12:39 PM, Teon Brooks <<a href="mailto:teon.brooks@gmail.com" target="_blank">teon.brooks@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">Hi David,<div><br></div><div>Currently, there isn't a way to baseline saved epochs file using mne.read_epochs. One temporary solution is to create the Epochs object from mne.read_epochs and take the data using epochs.get_data() and pass it to EpochsArray where you can specify a baseline.</div><div><br></div><div>If you could raise an issue on mne-python, we could consider adding baseline to the read_epochs function.</div><div><br></div><div>HTH,</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr">-teon</div></div>
<br><div class="gmail_quote">On Fri, Jul 10, 2015 at 11:35 AM, David I Leitman <span dir="ltr"><<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi all, <div><br></div><div> Quick question how can I baseline correct a 'fif 'file that contains epochs, I would like to read it in using mne.read_epochs and then apply a baseline correction and re save the file with a different name. The "epochs.baseline" seems to be empty as I get Type="NoneType"</div><div><br></div><div><br></div><div>thanks dave<br><div>
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Leitman PhD</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px"><br></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="'Lucida Grande'" size="2"><span style="font-size:10px">Research Assistant Professor</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Department of Psychiatry-</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Neuropsychiatry program</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Perelman School of Medicine</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">University of Pennsylvania</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Gates Pavilion 10th floor room 1042</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">3400 Spruce St</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Philadelphia, PA 19104-4283</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">P: <a href="tel:%28215%29%20662-7389" value="+12156627389" target="_blank">(215) 662-7389</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">F: <a href="tel:%28215%29%20662-7903" value="+12156627903" target="_blank">(215) 662-7903</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">E: <a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a></span></font></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span><span style="font-family:'Lucida Grande';font-size:x-small">Faculty page:<span style="white-space:pre-wrap"> </span></span><a href="http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343" style="font-size:11px" target="_blank">http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343</a><div><span style="font-family:'Lucida Grande';font-size:x-small">Lab website:</span></div><div><span style="font-family:'Lucida Grande';font-size:x-small"> </span><span style="font-family:'Lucida Grande';font-size:x-small"><a href="http://davidileitman.com/" target="_blank">http://davidileitman.com</a></span></div><div><br></div><div>The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. 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If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.</div><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="'Lucida Grande'" size="2"><span style="font-size:10px"><br></span></font></div></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></span><br>
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_______________________________________________<br>Mne_analysis mailing list<br><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br><br><br>The information in this e-mail is intended only for the person to whom it is<br>addressed. If you believe this e-mail was sent to you in error and the e-mail<br>contains patient information, please contact the Partners Compliance HelpLine at<br><a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>but does not contain patient information, please contact the sender and properly<br>dispose of the e-mail.<br></blockquote></div><br><div>
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">David I. Leitman PhD</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px"><br></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="'Lucida Grande'" size="2"><span style="font-size:10px">Research Assistant Professor</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Department of Psychiatry-</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Neuropsychiatry program</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Perelman School of Medicine</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">University of Pennsylvania</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Gates Pavilion 10th floor room 1042</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">3400 Spruce St</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Philadelphia, PA 19104-4283</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">P: <a href="tel:%28215%29%20662-7389" value="+12156627389" target="_blank">(215) 662-7389</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">F: <a href="tel:%28215%29%20662-7903" value="+12156627903" target="_blank">(215) 662-7903</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">E: <a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a></span></font></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span><span style="font-family:'Lucida Grande';font-size:x-small">Faculty page:<span style="white-space:pre-wrap"> </span></span><a href="http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343" style="font-size:11px" target="_blank">http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343</a><div><span style="font-family:'Lucida Grande';font-size:x-small">Lab website:</span></div><div><span style="font-family:'Lucida Grande';font-size:x-small"> </span><span style="font-family:'Lucida Grande';font-size:x-small"><a href="http://davidileitman.com" target="_blank">http://davidileitman.com</a></span></div><div><br></div><div>The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.</div><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-variant:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="word-wrap:break-word"><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="'Lucida Grande'" size="2"><span style="font-size:10px"><br></span></font></div></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></div></span><br></span><br>
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