<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@SimSun";
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:black;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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 Heather,<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 plugin (as I just tested on my laptop) does not to likelihood rejection by default (if you don’t click the “Reject..” button), so if you just click “Ok” in the main Amica gui dialog (without clicking “Reject..”), the input.param file will have “do_reject 0” etc., and there won’t be an data rejection.<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'>However, if you do click “Reject..”, the dialog box as shown on the Help page will come up, with “Reject unlikely data” checked, and the other default values you mentioned, and if you then click “Ok” to go back, and “Ok” to run, the rejection will be performed, with those reject values (reject 5 times, etc.), and the input.param file should correspond to those values.<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 even the values that appear in the dialog when you click “Reject..” are not the default values until you click “Reject..” If you do click “Reject..” then rejection will be performed with the values shown, unless you unclick “Reject unlikely data” before clicking Ok to go back.<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'>Hopefully that long-winded explanation is understandable and is the behavior you are able to verify as well.<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><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>Heather Lucas<br><b>Sent:</b> Friday, April 21, 2017 9:26 AM<br><b>To:</b> eeglablist@sccn.ucsd.edu<br><b>Subject:</b> [Eeglablist] amica1.5 - mismatch between GUI and input.param settings?<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hello all,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I recently began using amica1.5 as an eeglab plugin, and it appears to me that the parameter settings on the GUI don't all match up with the values in the corresponding input.param file. I have noticed this specifically for values pertaining to the rejection of unlikely data samples. For me, the default settings on the GUI are exactly as shown here:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="https://sccn.ucsd.edu/~jason/amica_help.html">https://sccn.ucsd.edu/~jason/amica_help.html</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>That is, the "Reject Unlikely Data Samples" box is checked, Num Reject is 5, Num LL stdev is 3, Start iter is 1, and Iter between rej is 0.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>However, when I run amica without changing any settings, the resulting input.param file lists the following:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>do_reject 0<o:p></o:p></p></div><div><p class=MsoNormal>numrej 3<o:p></o:p></p></div><div><p class=MsoNormal>rejsig 3.000000<o:p></o:p></p></div><div><p class=MsoNormal>rejstart 2<o:p></o:p></p></div><div><p class=MsoNormal>rejint 3<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Based on the runamica15 documentation, it seemed to me that these values should correspond to the 5 rejection-related GUI values. Am I misinterpreting something, and if so, could someone kindly explain what the differences are between these sets of parameters?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Many thanks,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best,<o:p></o:p></p></div><div><p class=MsoNormal>Heather<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><o:p> </o:p></p></div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <o:p></o:p></p><div><div><div><div><p class=MsoNormal>Heather Lucas, PhD<o:p></o:p></p></div><div><div><p class=MsoNormal><span style='color:black;background:black'>Postdoctoral Research Associate<br>Beckman Institute <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black;background:black'>University of Illinois Urbana-Champaign<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></div></div></body></html>