<div>Hi Odelia,</div>
<div> </div>
<div>Yes, I downloaded the latest version of Fieldtrip and tried your suggestion "cfg.neighbourdist = 0.03", but it still weirdly uses the far-away channels like A121 to do the channel-repair for A234 (these two channels are 24.1172cm apart!). Here is the detail:</div>
<div> </div>
<div>---------------------------</div>
<div>cfg = [];<br>cfg.dataset = 'e,rfhp0.1Hz'; </div>
<div>cfg.trialdef.eventtype = 'TRIGGER';<br>cfg.trialdef.eventvalue = 320; </div>
<div>cfg.trialdef.prestim = 1;<br>cfg.trialdef.poststim = 1;<br>cfg = ft_definetrial(cfg);<br>cfg.blc = 'yes'; % do baseline correction with the complete trial<br>
cfg.blcwindow = [-1 0];<br>cfg.channel = {'MEG'};<br>raw_DATA = ft_preprocessing(cfg);</div>
<div> </div>
<div> </div>
<div>cfg = [];<br>cfg.badchannel = {'A234'}; <br>cfg.neighbourdist = 0.03;<br>[raw_DATA] = ft_channelrepair(cfg, raw_DATA)</div>
<div> </div>
<div>---------------------------------------------------------------------</div>
<div> </div>
<div>And here is the outcome: -----------------------------</div>
<div><br>the input is raw data with 248 channels and 201 trials<br>repairing channel A234<br> using neighbour A121<br> using neighbour A143<br> using neighbour A173<br> using neighbour A8<br>repairing bad channels for trial 1<br>
repairing bad channels for trial 2<br>repairing bad channels for trial 3<br>repairing bad channels for trial 4<br>repairing bad channels for trial 5<br>repairing bad channels for trial 6<br>repairing bad channels for trial 7<br>
repairing bad channels for trial 8<br>repairing bad channels for trial 9<br>repairing bad channels for trial 10</div>
<div>....</div>
<div> </div>
<div>-------------------------</div>
<div> </div>
<div>Thank you.</div>
<div> </div>
<div>Jim<br><br></div>
<div class="gmail_quote">On Thu, Jun 30, 2011 at 4:04 AM, odelia nakar <span dir="ltr"><<a href="mailto:odidodi@hotmail.com">odidodi@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div dir="ltr">Hi Jim,<br><br>Try :<br>cfg.neighbourdist = 0.03;<br>I found it good for my data. (When you run the function the channels that repaired your data is displayed in the command window).<br><br>Good luck!<br>Odelia.<br>
<br><br>
<div>
<hr>
Date: Thu, 30 Jun 2011 01:05:08 -0500<br>From: <a href="mailto:megjim1@gmail.com" target="_blank">megjim1@gmail.com</a><br>To: <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>Subject: [FieldTrip] channelrepair issue
<div>
<div></div>
<div class="h5"><br><br>
<div>Dear all,</div>
<div> </div>
<div>We have 4D's WH3600 MEG system (248 channels) and we found the </div>
<div>-----------------</div>
<div><font face="Courier New" size="2"><font face="Courier New" size="2">cfg = [];<br>cfg.dataset = <br></font></font><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2">'e,rfhp0.1Hz'</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2">; </font></font><font face="Courier New" size="2"><font face="Courier New" size="2">cfg.trialdef.eventtype = </font></font><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2">'TRIGGER'</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2">;</font></font><br>
cfg.trialdef.eventvalue = <font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2">320; </font></font></font><br><font face="Courier New" size="2"><font face="Courier New" size="2">cfg.trialdef.prestim = 1</font></font><font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2">;</font></font></font><br>
<font face="Courier New" size="2"><font face="Courier New" size="2">cfg.trialdef.poststim = 1<br></font></font><font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2"><font face="Courier New" color="#228b22" size="2">;</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2"> cfg = ft_definetrial(cfg);<br>
cfg.blc = <br></font></font><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2">'yes'</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2">; </font></font><font face="Courier New" size="2"><font face="Courier New" size="2">cfg.blcwindow = [-1 0];</font></font><br>
cfg.channel = {<font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2">'MEG'</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2">};</font></font><br>
raw_DATA = ft_preprocessing(cfg);<br>raw_DATA.grad = ft_convert_units(raw_DATA.grad, <font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2"><font face="Courier New" color="#a020f0" size="2">'cm'</font></font></font><font face="Courier New" size="2"><font face="Courier New" size="2">)</font></font><br>
</div>
<div> </div>
<div>cfg = [];<br>cfg.badchannel = {'A234'};<br>[raw_DATA] = ft_channelrepair(cfg, raw_DATA)<br>the input is raw data with 248 channels and 201 trials<br>repairing channel A234<br> using neighbour A121<br> using neighbour A143<br>
using neighbour A154<br> using neighbour A173<br> using neighbour A224<br> using neighbour A8<br> using neighbour A91<br>repairing bad channels for trial 1<br>repairing bad channels for trial 2<br>repairing bad channels for trial 3</div>
<div>...</div>
<div>------------------------------------</div>
<div> </div>
<div>But channels like A121 and A143 are far away from the bad channel A234. How can they be used as neighbours (i.e. within 4cm, the default value for cfg.neighbourdist) for this bad channel?</div>
<div> </div>
<div>Any suggestions?</div>
<div> </div>
<div>Thanks a lot.</div>
<div> </div>
<div>Jim</div><br></div></div>_______________________________________________ fieldtrip mailing list <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
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</blockquote></div><br>