<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class="">just a couple of comments, since nobody chimes in :-)</div><div class="">
<br class=""><div><blockquote type="cite" class=""><div class="">Il giorno 16 feb 2016, alle ore 13:51, Seymour, Robert (Research Student) <<a href="mailto:seymourr@aston.ac.uk" class="">seymourr@aston.ac.uk</a>> ha scritto:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear all, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I am working with Elekta Neuromag data and want to load the raw .fif file into Fieldtrip; i.e. having not undergone Maxfilter cleaning. I have turned off Internal Active Sheilding (IAS) during recording.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Loading in motion-corrected data is fine and produces reasonable results. However using the same code with un-Maxfiltered data produces some very strange plots - please see some pictures I have uploaded online.. <a href="http://imgur.com/a/b0Mrl" id="LPlnk511218" title="http://imgur.com/a/b0Mrl
Ctrl+Click or tap to follow the link" class="">http://imgur.com/a/b0Mrl</a> . It is not an issue with the data themselves because it looks sensible in Graph (the Elekta data visualisation program). </div></div></div></blockquote><div><br class=""></div><div>They look reasonable ... what you see is the effect of the (bp?) filter on your data and the x seconds rectangular window that you’re using for watching at them. </div><div>The first pic should be grads, and the second mags, if I’m not mistaken, and in the second one you can clearly see 50 Hz mains noise (you’ve 50Hz over there, isn’t :-) ?!) </div><div>If you just want to take a look at the data and scroll trough the time, don’t apply “hardcoded” filters with ft_preprocessing, but fully exploit the power of ft_databrowser, and change filters on the fly there with the button on the right, using a cfg.preproc.xxx syntax. </div><div><br class=""></div><div>For a quick look at e.g. magnetometers, you can use:</div><div><br class=""></div><div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg = [];</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg.dataset= rawfile; <span style="color: #25992d" class="">%in your case</span></div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(178, 69, 243);" class=""><span style="color: #000000" class="">cfg.layout = </span>'neuromag306mag.lay'<span style="color: #000000" class="">;</span></div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg.channel = <span style="color: #b245f3" class="">'MEGMAG'</span>;</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">ft_databrowser(cfg)</div><div class=""><br class=""></div></div><div>check the help of ft_databrowser to see which option does what, but in this case the important part is cfg.dataset, that ft_databrowser uses to read directly the file from the disk. The additional stuff is for topoplotting on right click, e.g. to identify eye blinks …</div><div>The code above is not applying any filtering, so expect some mess, but then from the data browser click on the grey button on the right and try e.g.:</div><div><br class=""></div><div><p style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg.preproc.lpfilter = <span style="color: #b245f3" class="">'yes'</span> ; <span style="color: #25992d" class="">% you don't want to see 50 Hz now</span></p>
<p style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg.preproc.lpfreq = 45 ;</p>
<p style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier;" class="">cfg.preproc.hpfilter = <span style="color: #b245f3" class="">'yes'</span> ; </p>
<p style="margin: 0px; font-size: 10px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class=""><span style="color: #000000" class="">cfg.preproc.hpfreq = 1 ; </span>% try out different value, to suit your needs</p><div class=""><br class=""></div><div class=""><br class=""></div><div class="">then change a bit the values and see how this looks like. Then you can chop the data in epochs as you did (btw, there is no need of both cfg.headerfile and</div><div class="">cfg.datafile, the latter should suffice), but then again don’t apply any “hardcoded” filter values at this stage, if the idea is still to take a general look at the data. You can filter in plotting later … or just put the hardcoded filter values in your final (data in -> Nature paper out) script.</div><div class="">Hope this helps …</div><div class="">Best,</div><div class="">G.</div><div class=""><br class=""></div><div class=""><br class=""></div></div><blockquote type="cite" class=""><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">My preprocessing code can be loaded here:<span class="Apple-converted-space"> </span><a href="http://notepad.cc/peebluki61" id="LPlnk3819" class="">http://notepad.cc/peebluki61</a> . <span style="font-size: 12pt;" class="">If anyone has any idea what is going on I would be very grateful!</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Many thanks, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Robert Seymour (PhD student, Aston Brain Centre)</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:fieldtrip@donders.ru.nl" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">fieldtrip@donders.ru.nl</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div></blockquote><div><br class=""></div>Dr. Gianpaolo Demarchi<br class="">FB Psychologie - Universität Salzburg<div class="">Hellbrunnerstr, 34 5020 Salzburg (A)<br class="">Tel: +43 (0) 662 / 8044 - 5135<br class=""><a href="mailto:gianpaolo.demarchi@sbg.ac.at" class="">gianpaolo.demarchi@sbg.ac.at</a></div><br class=""></div><div><br class=""></div><br class=""></div></body></html>