<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi all,<div><br></div><div> I had a question about decimating an epochs file:</div><div><br></div><div>I am running the following algorithm below on a data file that is ~25 minutes long and sampled at 1000HZ :</div><div><br></div><div>I would like to decimate my data by 2 my data after I filter it using raw.filter(1, 80, method='iir')</div><div><br></div><div>Ideally I would like to hold off until after I find events and make the epoch file but before I apply the ICA as this causes me memory issues and is time consuming.</div><div><br></div><div>Can I just run "epochs.decim" after </div><div><span class="Apple-tab-span" style="white-space:pre"> </span>"epochs = mne.Epochs(raw, events, event_ids, tmin, tmax, proj=True, picks=picks,</div><div> baseline=None, preload=True, reject=reject, reject_tmin=reject_tmin, reject_tmax=reject_tmax)"</div><div><br></div><div>given the 'iir filtering I performed on the raw data? will it introduce any dsitortion or alliasing..., and if so should can I reapply a (~1-80 IIR filter) to deal with the distortion? </div><div><br></div><div>thanks //david</div><div><br></div><div>##### script</div><div><br></div><div><div>os.chdir(meg_dir)</div><div>raw_fname=dstraw_fname</div><div>raw=io.Raw(raw_fname,add_eeg_ref=False,preload=True)</div><div>raw.load_bad_channels(bad_file=bad_chan_fname,force=False)</div><div>raw.info</div><div><br></div><div>raw.info['bads'] += ['EEG001', 'EEG003']</div><div>picks = mne.pick_types(raw.info, meg=True, eeg=True, exclude='bads')</div><div><br></div><div>raw.filter(1, 80, method='iir')</div><div><br></div><div>events = mne.find_events(raw, stim_channel='STI101',shortest_event=1)</div><div>event_ids = {'stim_1': 5, 'stim_2': 6, 'stim_3': 7, 'stim_4': 8, 'stim_5': 9, 'stim_6': 10, 'stim_7': 11, 'stim_8': 12, 'stim_9': 13, 'stim_10': 14, 'stim_11': 15, 'stim_12': 16, 'stim_13': 17, 'stim_14': 18, 'stim_15': 19, 'stim_16': 20, 'stim_17': 21, 'stim_18': 22, 'stim_19': 23, 'stim_20': 24, 'stim_21': 25, 'stim_22': 26, 'stim_23': 27, 'stim_24': 28, 'stim_25': 29, 'stim_26': 30}</div><div><br></div><div>tmin, tmax, delay = -0.400, 1.9, 0.026 ## FOR BASELINED EPOCHS</div><div>reject_tmin, reject_tmax= -.200, 1.800</div><div>baseline = None # no baseline as high-pass is applied</div><div>reject = dict( grad= 9e-11, # T / m (gradiometers)</div><div> mag = 4.0e-12, # T (magnetometers)</div><div> eeg =200e-6, # (eeg channels)</div><div> )</div><div><br></div><div>epochs = mne.Epochs(raw, events, event_ids, tmin, tmax, proj=True, picks=picks,</div><div> baseline=None, preload=True, reject=reject, reject_tmin=reject_tmin, reject_tmax=reject_tmax)</div><div>######====>> put epochs.decim ? to decimate the data </div><div>ica = ICA(n_components=0.95).fit(raw, decim=6, reject=reject)</div><div>eog_epochs = create_eog_epochs(raw, ch_name='EOG', reject=reject)</div><div>eog_inds, eog_scores = ica.find_bads_eog(eog_epochs, ch_name='EOG')</div><div><br></div><div>ecg_epochs = create_ecg_epochs(raw, ch_name='ECG', reject=reject)</div><div>ecg_inds, ecg_scores = ica.find_bads_ecg(ecg_epochs, ch_name='ECG')</div><div><br></div><div>ica.plot_scores(eog_scores, eog_inds)</div><div>ica.plot_components(eog_inds)</div><div><br></div><div>ica.plot_scores(ecg_scores, ecg_inds)</div><div>ica.plot_components(ecg_inds)</div><div><br></div><div>eog_inds</div><div>ecg_inds</div><div>ica.exclude += eog_inds[:]</div><div>ica.exclude += ecg_inds[:]</div><div>ica.exclude</div><div>ica.plot_overlay(eog_epochs.average())</div><div>epochs_cln = ica.apply(epochs, copy=True)</div></div><div><br></div><div>#### script #####<br><div apple-content-edited="true">
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"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; 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Leitman PhD</span></font></div><div style="font-weight: normal; font-style: normal; font-family: Helvetica; font-size: 16px; "><font class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-span" style="font-size: 10px; "><br class="webkit-block-placeholder"></span></font></div><div style="font-weight: normal; font-style: normal; font-family: Helvetica; font-size: 16px; "><font class="Apple-style-span" face="'Lucida Grande'" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-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 class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-span" style="font-size: 10px; ">P: (215) 662-7389</span></font></div><div style="font-weight: normal; font-style: normal; font-family: Helvetica; font-size: 16px; "><font class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-span" style="font-size: 10px; ">F: (215) 662-7903</span></font></div><div style="font-weight: normal; font-style: normal; font-family: Helvetica; font-size: 16px; "><font class="Apple-style-span" face="Lucida Grande" size="2"><span class="Apple-style-span" style="font-size: 10px; ">E: <a href="mailto:leitman@mail.med.upenn.edu">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 class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: x-small; ">Faculty page:<span class="Apple-tab-span" style="white-space: pre; "> </span></span><a href="http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343" style="font-size: 11px; ">http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343</a><div><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: x-small; ">Lab website:</span></div><div><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: x-small; "> </span><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: x-small; "><a href="http://davidileitman.com">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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