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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 Tom,<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'>Could you try setting the flag do_opt_block = 0, in runamica12.m? Or download the most recent runamica12.m which has this as default (and as a flag option):<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'><a href="http://sccn.ucsd.edu/~jason/amica12/runamica12.m">http://sccn.ucsd.edu/~jason/amica12/runamica12.m</a>.<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'> It seems to be dying when determining the block size (trying different size blocks).<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'>Also, the eigenvalues of the data seem to indicate that the data is not conditioned very well. You might consider removing bad channels, then doing average reference, then high pass filtering first in eeglab if you haven’t already:<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'> % … remove bad channels …<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> EEG = pop_reref( EEG, ‘average’ );<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> EEG = pop_eegfilt( EEG, 1.0, 0, [], [0] );<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> [EEG.icaweights, EEG.icasphere, mods] = runamica12( EEG.data(:,:) );<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><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><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"'> Tom Campbell [mailto:tom_campbell75@hotmail.com] <br><b>Sent:</b> Tuesday, May 22, 2012 8:59 AM<br><b>To:</b> japalmer@ucsd.edu; send2zohre@yahoo.com; eeglab list; Katsumi Minakata<br><b>Subject:</b> RE: [Eeglablist] Running AMICA<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br></span><span style='font-family:"Calibri","sans-serif"'>Hello, In case recent developments helped, I ran an svn update of EEGLAB and then tried this under windows 7, 64-bit with 7.11.0.584 (R2010b) using amica12 of 3rd March, 2012 :</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br> <br></span><span style='font-family:"Calibri","sans-serif"'>>> [EEG.icaweights, EEG.icasphere, mods] = runamica12(EEG.data(:,:));<br>The system cannot find the path specified. <br>The system cannot find the path specified. <br>The system cannot find the path specified. <br>No recognized parallel environment found. Run qconf -spl to get a list of available environments and use keyword use_pe.<br>Running locally ...<br>Writing data file: C:\tom\MotParEEG\code\tmpdata39223.fdt<br>A subdirectory or file C:\tom\MotParEEG\code\amicaouttmp\ already exists. <br> 1 processor name = cvcn-PC.psydomain.psych.ndsu.nodak.edu <br> 1 host_num = -988751630 <br> This is MPI process 1 of 1 ; I am process 1 of <br> 1 on node: cvcn-PC.psydomain.psych.ndsu.nodak.edu <br> 1 : node root process 1 of 1 <br>Processing arguments ... <br> num_files = 1 <br> FILES: <br> C:\tom\MotParEEG\code\tmpdata39223.fdt <br> num_dir_files = 1 <br> initial matrix block_size = 128 <br> do_opt_block = 1 <br> number of models = 1 <br> number of density mixture components = 3 <br> pdf type = 0 <br> max_iter = 2000 <br> num_samples = 1 <br> data_dim = 168 <br> field_dim = 630432 <br> do_history = 0 <br> histstep = 10 <br> share_comps = 0 <br> share_start = 100 <br> comp_thresh = 0.990000000000000 <br> share_int = 100 <br> initial lrate = 0.100000000000000 <br> minimum lrate = 1.000000000000000E-008 <br> lrate factor = 0.500000000000000 <br> initial rholrate = 5.000000000000000E-002 <br> rho0 = 1.50000000000000 <br> min rho = 1.00000000000000 <br> max rho = 2.00000000000000 <br> rho lrate factor = 0.500000000000000 <br> kurt_start = 3 <br> num kurt = 5 <br> kurt interval = 1 <br> do_newton = 1 <br> newt_start = 50 <br> newt_ramp = 10 <br> initial newton lrate = 1.00000000000000 <br> do_reject = 0 <br> num reject = 3 <br> reject sigma = 3.00000000000000 <br> reject start = 2 <br> reject interval = 3 <br> max_thrds = 2 <br> write step = 10 <br> write_nd = 0 <br> write_LLt = 1 <br> dec window = 1 <br> max_decs = 3 <br> fix_init = 0 <br> update_A = 1 <br> update_c = 1 <br> update_gm = 1 <br> update_alpha = 1 <br> update_mu = 1 <br> update_beta = 1 <br> invsigmax = 100.000000000000 <br> invsigmin = 0.000000000000000E+000 <br> do_rho = 1 <br> load_rej = 0 <br> load_c = 0 <br> load_gm = 0 <br> load_alpha = 0 <br> load_mu = 0 <br> load_beta = 0 <br> load_rho = 0 <br> load_comp_list = 0 <br> do_mean = 1 <br> do_sphere = 1 <br> doPCA = 1 <br> pcadb = 30.0000000000000 <br> byte_size = 4 <br> doscaling = 1 <br> scalestep = 1 <br>A subdirectory or file C:\tom\MotParEEG\code\amicaouttmp\ already exists. <br> output directory = C:\tom\MotParEEG\code\amicaouttmp\ <br> 1 : setting num_thrds to 2 ... <br> 1 : using 2 threads. <br> 1 : node_thrds = 2 <br> bytes in real = 1 <br> 1 : REAL nbyte = 1 <br> getting segment list ... <br> blocks in sample = 630432 <br> total blocks = 630432 <br> node blocks = 630432 <br> node 1 start: file 1 sample 1 index <br> 1 <br> node 1 stop : file 1 sample 1 index <br> 630432 <br> 1 : data = 1.56996321678162 4.14537906646729 <br> getting the mean ... <br> mean = 17.8814622999107 4.04874815379699 <br> 4.16267016630081 <br> subtracting the mean ... <br> getting the sphering matrix ... <br> cnt = 630432 <br> doing eig nx = 168 lwork = 282240 <br> minimum eigenvalues = -1.057109602531463E-008 -2.148912456381678E-011 <br> 5.144711324023235E-012 <br> maximum eigenvalues = 161054352.523510 102447610.050744 <br> 1207240.45212326 <br> num eigs kept = 166 <br> numeigs = 166 <br> sphering the data ... <br> 1 Allocating variables ... <br> 1 : Initializing variables ... <br> 1 : Determining optimal block size .... </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br> <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> {There is then a popup that says amica12win64.exe has stopped working, with a cancel box, followed by a similar box with a close program button}<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>On pressing 'close program' there is then the error:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>No gm present, setting num_models to 1<br>No W present, exiting<br>??? Reference to non-existent field 'W'.<br>Error in ==> runamica12 at 858<br> weights = mods.W(:,:,1);<br> <br>A similar problem happens with </span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>runamica12 using epoched or continuous data. I previously tried using the dos version of the program and tinkering with the parameters in the .param with more success (this may be rather unwise for the uninitiated like myself when runamica12 might do this rather better), but with some .fdt, I found AMICA will not process that data with many different errors depending </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>on the choice of parameters, when infomax will process the same data. <br> <br>I really don't want to give up on this as done properly I can see it is about the best way to do ica of EEG. Hoping for a simple fix...<o:p></o:p></span></p><div><div id=SkyDrivePlaceholder><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Best regards,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Tom<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p></div><div class=MsoNormal align=center style='text-align:center'><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><hr size=2 width="100%" align=center></span></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From: </span><a href="mailto:japalmer29@gmail.com"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>japalmer29@gmail.com</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br>To: </span><a href="mailto:send2zohre@yahoo.com"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>send2zohre@yahoo.com</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>; </span><a href="mailto:eeglablist@sccn.ucsd.edu"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>eeglablist@sccn.ucsd.edu</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br>Date: Tue, 22 May 2012 00:05:43 -0700<br>Subject: Re: [Eeglablist] Running AMICA<o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Hi Zohre,</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>The matlab programs amica_ex.m and amica10.m are mainly for demo purposes. If you use runamica12.m (</span><a href="http://sccn.ucsd.edu/~jason/amica_web.html" target="_blank"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>http://sccn.ucsd.edu/~jason/amica_web.html</span></a><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> ) to run one of the binaries, the following should load the output into eeglab:</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> >> [EEG.icaweights, EEG.icasphere, mods] = runamica12(EEG.data(:,:));</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> >> EEG = eeg_checkset(EEG);</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> >> eeglab redraw</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Runamica12.m tries to figure out if you’re running pc, mac, or linux, and use the appropriate 32 bit or 64 bit version (assuming you downloaded one of these from the links on the webpage.)</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Best,</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Jason</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><div><div style='border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-color:currentColor currentColor'><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"'> </span><a href="mailto:eeglablist-bounces@sccn.ucsd.edu"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>eeglablist-bounces@sccn.ucsd.edu</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span><a href="mailto:[mailto:eeglablist-bounces@sccn.ucsd.edu]"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>[mailto:eeglablist-bounces@sccn.ucsd.edu]</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <b>On Behalf Of </b>Zohre Zakeri<br><b>Sent:</b> Friday, May 18, 2012 8:48 AM<br><b>To:</b> </span><a href="mailto:eeglablist@sccn.ucsd.edu"><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>eeglablist@sccn.ucsd.edu</span></a><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><br><b>Subject:</b> [Eeglablist] Running AMICA<o:p></o:p></span></p></div></div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <o:p></o:p></span></p><div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Hi all,</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>I am trying to run AMICA algorithm in matlab on EEG data.</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>I found amica_ex.m and amica10.m (which is older).</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>I also used this command to get the components, which I found in the websie:</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> EEG.icawinv=pinv(EEG.icaweights);<br> EEG.icasphere = eye(size(EEG.icaweights));<br> [EEG.icaact] = eeg_getica(EEG,1:EEG.nbchan);</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>however, it doesn't work and I don't have any idea to work with this algorithm and get</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>independent components as outpt.</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>can anyone help?</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p></div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Thanks all,<br><br>zohre</span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p></o:p></span></p><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'> </span><span 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