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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Hi Cortney,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>The sphering matrix used in the dimensionality reduction case is the first num_pcs rows of the sphering matrix.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>So the ICA unixing matrix would be<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> >> numpcs = 150;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> >> activations = weights * sphere(1:numpcs,:) * (input_data – row_means);<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Jason<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> eeglablist-bounces@sccn.ucsd.edu [mailto:eeglablist-bounces@sccn.ucsd.edu] <b>On Behalf Of </b>Cortney Bradford<br><b>Sent:</b> Tuesday, March 12, 2013 12:36 PM<br><b>To:</b> eeglablist@sccn.ucsd.edu<br><b>Subject:</b> [Eeglablist] AMICA - Using PCA parameter<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>We are interested in using using the PCA parameter when running AMICA (amica11).<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>sample of the parameter settings:<o:p></o:p></p></div><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>data_dim 229<o:p></o:p></p></div><div><p class=MsoNormal>doPCA 1<o:p></o:p></p></div><div><p class=MsoNormal>pcakeep 150<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>AMICA seemed to run fine, but produced an ICA weights matrix that is 150x150 and sphere matrix that is 229x229. This becomes a problem when we try to compute the activations using the following equation, due to the matrices being different sizes. <o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><pre style='background:#FFFFDD'><b><span style='font-family:Courier;color:blue'>activations = weights*sphere*(input_data - row_means);</span></b><span style='color:#DD6A66'><o:p></o:p></span></pre><pre style='background:#FFFFDD'><b><span style='font-family:Courier;color:blue'><br><br><o:p></o:p></span></b></pre><pre style='background:#FFFFDD'><span style='font-family:"Arial","sans-serif"'>Are we doing something wrong in setting parameters or is this a bug?</span><o:p></o:p></pre><pre style='background:#FFFFDD'><o:p> </o:p></pre><pre style='background:#FFFFDD'><span style='font-family:"Arial","sans-serif"'>Thank you,</span><o:p></o:p></pre><pre style='background:#FFFFDD'><o:p> </o:p></pre><pre style='background:#FFFFDD'><span style='font-family:"Arial","sans-serif"'>J. Cortney Bradford</span><o:p></o:p></pre><pre style='background:#FFFFDD'><span style='font-family:"Arial","sans-serif"'>Post-doc</span><o:p></o:p></pre><pre style='background:#FFFFDD'><o:p> </o:p></pre><pre style='background:#FFFFDD'><span style='font-family:"Arial","sans-serif"'>University of Michigan</span><o:p></o:p></pre><pre style='background:#FFFFDD'><b><span style='font-family:Courier;color:blue'><br><br><o:p></o:p></span></b></pre><pre style='background:#FFFFDD'><b><span style='font-family:Courier;color:blue'><br><br><o:p></o:p></span></b></pre><pre style='background:#FFFFDD'><span style='color:#DD6A66'><o:p> </o:p></span></pre><pre style='background:#FFFFDD'><o:p> </o:p></pre><pre style='background:#FFFFDD'><o:p> </o:p></pre><pre style='background:#FFFFDD'><span style='color:#DD6A66'><o:p> </o:p></span></pre><pre style='background:#FFFFDD'><span style='color:#DD6A66'><o:p> </o:p></span></pre><pre style='background:#FFFFDD'><span style='color:#DD6A66'><o:p> </o:p></span></pre></div></div></body></html>