<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Barbara,<div><br></div><div>Good plan to adjust the code a bit in this respect. Could you please file a bug about this on our bugzilla list: <a href="http://bugzilla.fcdonders.nl">bugzilla.fcdonders.nl</a></div><div><br></div><div>Best wishes,</div><div><br></div><div>Jan-Mathijs</div><div><br></div><div><br><div><div>On Apr 19, 2012, at 8:59 AM, Barbara Haendel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br><br>Hey there, thanks a lot for the replies!<br><br>Panagiotis hit the mark. Indeed the reference channels were excluded in the first round of preprocessing. May be one could include a short note on that in the ft_denoise m-file description since only including relevant channels is the normal way to treat data in preprocessing. <br><br>Thanks again,<br>Barbara<br><br><br><br><br>-------- Original-Nachricht --------<br><blockquote type="cite">Datum: Mon, 16 Apr 2012 17:53:56 +0200<br></blockquote><blockquote type="cite">Von: Panagiotis Tsiatsis <<a href="mailto:Panagiotis.Tsiatsis@Tuebingen.MPG.de">Panagiotis.Tsiatsis@Tuebingen.MPG.de</a>><br></blockquote><blockquote type="cite">An: Email discussion list for the FieldTrip project <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br></blockquote><blockquote type="cite">Betreff: Re: [FieldTrip] ft_denoise_synthetic 3rd order grad<br></blockquote><br><blockquote type="cite">Hello girls and guys,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It is working for my CTF MEG data - the version that I have is v4692 <br></blockquote><blockquote type="cite">2011-11-07.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The other thing that might cause a problem could be ommiting the <br></blockquote><blockquote type="cite">reference channels definition before the ft_ preprocessing command that <br></blockquote><blockquote type="cite">gave you your "dataprepro"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">i.e maybe you might need something like this<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cfg = [];<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite">//various preprocessing parameters<br></blockquote><blockquote type="cite">...<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cfg.channel = {'MEG', 'MEGREF', 'REFGRAD' , 'REFMAG'};<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">dataprepro = ft_preprocessing(cfg);<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hope you are lucky :)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Panagiotis<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 4/16/2012 4:59 PM, Stan van Pelt wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Barbara,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I can replicate your finding, but am unsure what is causing it. Maybe <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the difference/correction is lower than the Matlab or CTF precision? <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">In any case, if the 3rd order gradients were on, ft_denoise_synthetic <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">would undo the G3BR-balancing, ergo it toggles.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Best,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Stan<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">------------------------------------------------------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Van: *"Michael Wibral" <<a href="mailto:michael.wibral@web.de">michael.wibral@web.de</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Aan: *"Email discussion list for the FieldTrip project"<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Verzonden: *Maandag 16 april 2012 16:46:27<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Onderwerp: *Re: [FieldTrip] ft_denoise_synthetic 3rd order grad<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi Barbara,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> are you certain that the original data do not have 3rd gradients<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> enabled? - looking at them once in dataEditor, switching to 3rd<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> grads and accidentally forgetting to unclick 'save parameters with<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> dataset' will make them have 3rd grads...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> When I last used ft_denoise_synthetic it worked pretty much as<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> described (??).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Michael<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Gesendet:* Montag, 16. April 2012 um 15:56 Uhr<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Von:* "Barbara Haendel" <<a href="mailto:B.Haendel@gmx.net">B.Haendel@gmx.net</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *An:* <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> *Betreff:* [FieldTrip] ft_denoise_synthetic 3rd order grad<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Dear fieldtrip users,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> has anyone experience in using ft_denoise_synthetic? If I try to<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> calculate 3rd order grads in the below specified way the data does<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> not change with respect to the input data (which has no synthetic<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> gradiometer applied). Is there some obvious misunderstanding on my<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> side of how to use this function or is our environment truly<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> noiseless :)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Cheers,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Barbara<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> cfg=[];<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> cfg.gradient ='G3BR';<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> cfg.trials = 'all';<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> data_3rdorder = ft_denoise_synthetic(cfg, dataprepro);<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">data_3rdorder.grad.balance<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ans =<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> G1BR: [1x1 struct]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> G2BR: [1x1 struct]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> G3BR: [1x1 struct]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> current: 'G3BR'<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> previous: {'none'}<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sum(dataprepro.trial{8}(30,:)-data_3rdorder.trial{8}(30,:))<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ans = 0<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> -- <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Jetzt informieren:<br></blockquote></blockquote><blockquote type="cite"><a href="http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a">http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a</a><br></blockquote><blockquote type="cite"><blockquote type="cite"> _______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> fieldtrip mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> _______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> fieldtrip mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-- <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Stan van Pelt<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Donders Institute for Brain, Cognition and Behaviour, Radboud <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">University Nijmegen<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Kapittelweg 29, 6525 EN Nijmegen, Netherlands<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">E-mail: <a href="mailto:stan.vanpelt@donders.ru.nl">stan.vanpelt@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Website: <a href="http://www.ru.nl/donders/">www.ru.nl/donders/</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Phone: (+31) (0)24 36 10981<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Fax: (+31) (0)24 36 10989<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">fieldtrip mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">Panagiotis S. Tsiatsis<br></blockquote><blockquote type="cite">Max Planck Institute for Biological Cybernetics<br></blockquote><blockquote type="cite">Cognitive NeuroImaging Group<br></blockquote><blockquote type="cite">Tuebingen, Germany<br></blockquote><blockquote type="cite"><br></blockquote><br>-- <br>NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! <br>Jetzt informieren: <a href="http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a">http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a</a><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div></div></span></div></span></div></span></div></span></div></span></span>
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