<div dir="ltr">Dear Srinivas,<div><br></div><div><div>> 1. high pass filter (1Hz)</div><div>2. line noise filter</div><div>3. bad channel rejection </div><div>4. common average reference</div><div>5. Artifact subspace reconstruction</div><div>6. AMICA</div><div>7. Apply ICA sphering and weighting matrices to data </div></div><div><br></div><div>I recommend average reference AFTER ASR (and before AMICA, reject 1 channel or reduce rank by 1 with PCA option.)</div><div><br></div><div>If the number of channels are different, you can't apply AMICA weight matrices.</div><div><br></div><div>> Let say, after step 5, I have 66 channels and ASR rejects one channel. I get an error when I try to apply sphering and weighting matrices on non-ASR cleaned data because icasphere and icaweights are matrices of size 65 by 65. To avoid this problem, should I remove that bad electrode prior average reference so that ASR would not reject any electrodes?<br></div><div><br></div><div>I assume you want to load AMICA results to the ASR-cleaned data. So no problem. It's not that clean_rawdata() channel rejection confuses the number of channels. It just reject bad channels.</div><div><br></div><div>Makoto</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 29, 2015 at 8:47 AM, Srinivas Kota <span dir="ltr"><<a href="mailto:svkota@gmail.com" target="_blank">svkota@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">Hello<div><br></div><div>My EEG data consists of 71 channel and of 15 minutes duration with a sampling rate of 1000 Hz. The preprocessing pipeline include</div><div>1. high pass filter (1Hz)</div><div>2. line noise filter</div><div>3. bad channel rejection </div><div>4. common average reference</div><div>5. Artifact subspace reconstruction</div><div>6. AMICA</div><div>7. Apply ICA sphering and weighting matrices to data </div><div><br></div><div>Should I consider ASR cleaned data or average referenced data (prior ASR) for applying ICA sphering and weighting matrices? Any explanation would be helpful.</div><div><br></div><div>Let say, after step 5, I have 66 channels and ASR rejects one channel. I get an error when I try to apply sphering and weighting matrices on non-ASR cleaned data because icasphere and icaweights are matrices of size 65 by 65. To avoid this problem, should I remove that bad electrode prior average reference so that ASR would not reject any electrodes?</div><div><br></div><div>Best</div><div>Srini<br clear="all"><div><br></div>-- <br><div><div dir="ltr"><br>***********************************************************<div>Srinivas Kota, Ph.D<br>Research Scientist<br>Movement and Neurosciences Center<br>Institute for Rehabilitation Science and Engineering<br>Madonna Rehabilitation Hospital<br>5401 South St, Lincoln, NE 68506<br>Email: <a href="mailto:svkota@gmail.com" target="_blank">svkota@gmail.com</a><br>Ph: <a value="+16183190471">(618) 319-0471</a> (cell)<font color="#3F0080" face="Comic Sans MS,sans-serif" size="2"><span style="font-size:14px"><font color="black" face="Tahoma" size="2"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial"><font size="2"><br><a href="https://owa.madonna.org/owa/redir.aspx?C=RNnR5lrQvEmYU7lVtl6kLHIjwe3PiNAI8ouI90lD2Vnn4niuQ5QMBdLYDKmByFhfb525xS5XXT8.&URL=http%3a%2f%2fwww.madonna.org%2fresearch_institute%2findex.html" target="_blank"><font face="Tahoma"><font size="3"><span style="font-size:12pt" lang="en">www.madonna.org/research_institute/index.html</span></font></font></a><font face="Tahoma"><span lang="en">
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