<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Rajat,<div><br></div><div>what do you mean by "way too long"?</div><div><br></div><div>Have you tried setting the resolution of the mesh in the call to ft_prepare_mesh prior to ft_prepare_headmodel?</div><div><div apple-content-edited="true"><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><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 12px; "><br></div></div></span></div><div><div>Setting it to cfg.resolution = 5 (which changes the mesh resolution from the default 1mm to 5mm) greatly sped up the mesh preparation and leadfield computation in my case.</div><div>Please beware however that I use a rather old FT-Version as I don't have a current Matlab Version, so the functionality might have changed.</div><div><br></div><div>Good Luck,</div><div><br></div><div>Julian</div><div><br></div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 12px; ">********************</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><b>Dr. Julian Keil</b></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><b><br></b></div>AG Multisensorische Integration<br>Psychiatrische Universitätsklinik<br>der Charité im St. Hedwig-Krankenhaus<br>Große Hamburger Straße 5-11, Haus 2<br>10115 Berlin</div><div><br>Telefon: +49-30-2311-1879<br>Fax: +49-30-2311-2209 </div><div><a href="http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration">http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration</a></div></div><div><br></div><div>Am 13.04.2016 um 16:25 schrieb Rajat Thomas:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>Last week I asked for help with Simbio and after following the suggestion of volume reslicing magically the<br>simbio based headmodel was created.<br><br>But my leadfield calculations are taking way too long.<br>It is a 128^3 grid and am running it on my desktop. (2.4 GHz, plenty of memory 32GB)<br><br>Could anyone give me a rough ball park on how long it should take to create a leadfield?<br><br>Thank you.<br>Rajat<br><br><br><br>Rajat Mani Thomas<br>Social Brain Lab<br>Netherlands Institute for Neuroscience<br>Amsterdam<br><br>________________________________________<br>From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>> on behalf of <a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> <<a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>><br>Sent: 08 April 2016 12:00<br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>Subject: fieldtrip Digest, Vol 65, Issue 7<br><br>Send fieldtrip mailing list submissions to<br> <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>or, via email, send a message with subject or body 'help' to<br> <a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a><br><br>You can reach the person managing the list at<br> <a href="mailto:fieldtrip-owner@science.ru.nl">fieldtrip-owner@science.ru.nl</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of fieldtrip digest..."<br><br><br>Today's Topics:<br><br> 1. Re: FEM using Simbio (Johannes Vorwerk)<br> 2. Re: FEM using Simbio (Cristiano Micheli)<br> 3. Dipole fitting (Giovanni Pellegrino)<br> 4. Birmingham-Illinois BRIDGE Fellowships (Ole Jensen)<br> 5. Using FieldTrip to analyse LFP recordings in rat<br> (<a href="mailto:laetitia.lalla@inserm.fr">laetitia.lalla@inserm.fr</a>)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 7 Apr 2016 14:25:42 +0200<br>From: Johannes Vorwerk <<a href="mailto:j.vorwerk@uni-muenster.de">j.vorwerk@uni-muenster.de</a>><br>To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>Subject: Re: [FieldTrip] FEM using Simbio<br>Message-ID: <<a href="mailto:435735E3-7D87-4DD6-A2C1-E2BBFBBF4B44@googlemail.com">435735E3-7D87-4DD6-A2C1-E2BBFBBF4B44@googlemail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi,<br><br>this question was already answered in this thread<br><br><a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html</a> <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html</a>><br><br>If ft_volumereslice is not applied before the mesh generation, the afterwards applied transformation might flip the directions of the mesh, leading to the described error.<br><br>Best,<br> Johannes<br><br><blockquote type="cite">Am 06.04.2016 um 16:03 schrieb Carsten Wolters <<a href="mailto:carsten.wolters@uni-muenster.de">carsten.wolters@uni-muenster.de</a>>:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Dear Rajat,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">the element-node cards of SimBio-NeuroFEM need to follow certain orientations (see <a href="http://www.simbio.de">www.simbio.de</a> <<a href="http://www.simbio.de/">http://www.simbio.de/</a>>).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If you do not want to struggle with meshing/ordering, use the SimBio-VGRID mesher<br></blockquote><blockquote type="cite"><a href="http://vgrid.simbio.de/">http://vgrid.simbio.de/</a> <<a href="http://vgrid.simbio.de/">http://vgrid.simbio.de/</a>><br></blockquote><blockquote type="cite">that follows the required ordering of nodes. You might use this mesher to produce 1mm geometry-adapted FEM meshes<br></blockquote><blockquote type="cite">that show good overall performance, see<br></blockquote><blockquote type="cite"><a href="http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf</a> <<a href="http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf</a>><br></blockquote><blockquote type="cite">and<br></blockquote><blockquote type="cite"><a href="http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf</a> <<a href="http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf">http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf</a>><br></blockquote><blockquote type="cite">(latter was just accepted by NeuroImage).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best regards<br></blockquote><blockquote type="cite"> Carsten<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Am 06.04.2016 um 15:10 schrieb Rajat Thomas:<br></blockquote><blockquote type="cite"><blockquote type="cite">Dear all,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Has anyone used the FEM approach to Headmodels using Simbio recently?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If so, I get this error:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"Elements have wrong orientation or are degenerated"<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Any ideas?<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.method ='simbio';<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows mesh.tissyelabel<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">vol = ft_prepare_headmodel(cfg, mesh);<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">And;<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">disp(mesh)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> hex: [545883x8 double]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> pnt: [569722x3 double]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> labels: [545883x1 double]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> tissue: [545883x1 double]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> unit: 'mm'<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> cfg: [1x1 struct]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Any help would be highly appreciated.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Rajat<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"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Rajat Mani Thomas<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Social Brain Lab<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Netherlands Institute for Neuroscience<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Amsterdam<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> <<a href="mailto:fieldtrip@donders.ru.nl">mailto: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> <<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"><carsten_wolters.vcf>_______________________________________________<br></blockquote><blockquote type="cite">fieldtrip mailing list<br></blockquote><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a> <<a href="mailto:fieldtrip@donders.ru.nl">mailto:fieldtrip@donders.ru.nl</a>><br></blockquote><blockquote type="cite"><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a> <<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a>><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/2ea995ee/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/2ea995ee/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 7 Apr 2016 17:36:37 +0200<br>From: Cristiano Micheli <<a href="mailto:michelic72@gmail.com">michelic72@gmail.com</a>><br>To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>Subject: Re: [FieldTrip] FEM using Simbio<br>Message-ID:<br> <<a href="mailto:CADW7XCAQONsZ_ujPhkffskZ+j-mnHnAzunS68CdKU6MLSosUPA@mail.gmail.com">CADW7XCAQONsZ_ujPhkffskZ+j-mnHnAzunS68CdKU6MLSosUPA@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi Rajat<br><br>My guess is that the orientations of your hexahedrons are not correct.<br>According to a low-level file's internal rules, elements' orientations have<br>to abide strict rules (not sure what exactly the contraints are in this<br>case though...).<br>I had same problems when for example the triangular boundaries used to<br>define the 3d hexahedral mesh were not topologically correct, to start with.<br>Admittedly this approach requires a lot of technical expertise.<br>Can I ask you what do you need a FEM model for?<br><br>Regards<br>Cris Micheli<br><br><br><br><br>On Wed, Apr 6, 2016 at 3:10 PM, Rajat Thomas <<a href="mailto:r.thomas@nin.knaw.nl">r.thomas@nin.knaw.nl</a>> wrote:<br><br><blockquote type="cite">Dear all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Has anyone used the FEM approach to Headmodels using Simbio recently?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If so, I get this error:<br></blockquote><blockquote type="cite">"Elements have wrong orientation or are degenerated"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any ideas?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cfg = [];<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cfg.method ='simbio';<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows<br></blockquote><blockquote type="cite">mesh.tissyelabel<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">vol = ft_prepare_headmodel(cfg, mesh);<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">And;<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">?<br></blockquote><blockquote type="cite">disp(mesh)<br></blockquote><blockquote type="cite"> hex: [545883x8 double]<br></blockquote><blockquote type="cite"> pnt: [569722x3 double]<br></blockquote><blockquote type="cite"> labels: [545883x1 double]<br></blockquote><blockquote type="cite"> tissue: [545883x1 double]<br></blockquote><blockquote type="cite"> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}<br></blockquote><blockquote type="cite"> unit: 'mm'<br></blockquote><blockquote type="cite"> cfg: [1x1 struct]<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any help would be highly appreciated.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Rajat<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Rajat Mani Thomas<br></blockquote><blockquote type="cite">Social Brain Lab<br></blockquote><blockquote type="cite">Netherlands Institute for Neuroscience<br></blockquote><blockquote type="cite">Amsterdam<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">fieldtrip mailing list<br></blockquote><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote><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 type="cite"><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/4adfe55a/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/4adfe55a/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 7 Apr 2016 15:02:05 -0400<br>From: Giovanni Pellegrino <<a href="mailto:giovannipellegrino@gmail.com">giovannipellegrino@gmail.com</a>><br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>Subject: [FieldTrip] Dipole fitting<br>Message-ID:<br> <<a href="mailto:CAN6FyLVw=e7gOOvGDo47fT3j0frr8FUAEcsm55O8ZzqA=u8GDw@mail.gmail.com">CAN6FyLVw=e7gOOvGDo47fT3j0frr8FUAEcsm55O8ZzqA=u8GDw@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Dear Fieldtrippers,<br><br>Do you know if the FieldTrip Dipole Fitting has been compared to the CTF,<br>Elekta, BESA or Curry? Are you aware of any study on this topic?<br><br>Thanks in advance for your help<br><br>Giovanni<br><br>--<br>Giovanni Pellegrino, MD<br>Multimodal Functional Imaging Laboratory<br>Montreal Neurological Institute, McGill University<br>Address: 332 Duff Medical Building, 3775 rue University, Montreal, QC, H3A<br>2B4, Canada<br>Phone: (514) 398?1678<br>Fax: (514) 398?7461<br>Email: <a href="mailto:giovannipellegrino@gmail.com">giovannipellegrino@gmail.com</a>, <a href="mailto:giovanni.pellegrino2@mcgill.ca">giovanni.pellegrino2@mcgill.ca</a><br>Homepage: <a href="http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleGiovanni">http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleGiovanni</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/d01144bd/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160407/d01144bd/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 4<br>Date: Fri, 8 Apr 2016 09:23:46 +0200<br>From: Ole Jensen <<a href="mailto:ole.jensen@donders.ru.nl">ole.jensen@donders.ru.nl</a>><br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>Subject: [FieldTrip] Birmingham-Illinois BRIDGE Fellowships<br>Message-ID: <<a href="mailto:57075C82.8030309@donders.ru.nl">57075C82.8030309@donders.ru.nl</a>><br>Content-Type: text/plain; charset=utf-8; format=flowed<br><br>Dear all,<br><br>I would like to point you to a set of Birmingham-Illinois BRIDGE<br>Fellowships providing some exciting research and career prospects:<br><a href="http://www.birminghamillinoisbridge.org/index.php/fellows/">http://www.birminghamillinoisbridge.org/index.php/fellows/</a><br><br>In particular the areas 'Cognition and Ageing' and 'Brain Trauma' could<br>be relevant for candidates with EEG/MEG expertise.<br><br>All the best,<br><br>Ole<br><br>--<br>Prof. dr. Ole Jensen<br>http://www.neuosc.com<br><br><br><br>------------------------------<br><br>Message: 5<br>Date: Fri, 08 Apr 2016 10:27:58 +0200<br>From: laetitia.lalla@inserm.fr<br>To: fieldtrip@science.ru.nl<br>Subject: [FieldTrip] Using FieldTrip to analyse LFP recordings in rat<br>Message-ID: <628babdc107aebd4cc7588ea87ce5ea6@inserm.fr><br>Content-Type: text/plain; charset="utf-8"<br><br><br><br>Hello everyone,<br><br>my name is Laetitia and I'm a Phd student in Marseille (France). I'm<br>doing in-vivo recording in freely-moving rats : I implant them with 2<br>electrodes deep into 2 different regions of the brain. I'm studying the<br>Local Field Potentials and I want to use FieldTrip to analyse the data.<br><br>To simplify :<br><br>- I have 2 rats.<br><br>- Each rat did 20 sessions of the task (on 20 different days).<br><br>- Each session consists of 20 trials of condition 1 and 20 trials of<br>condition 2.<br><br>I have 2 questions.<br><br>1) I have the feeling it would be meaningless to do "source<br>reconstruction" because my electrodes are already deep inside my<br>"source" and the LFP I am recording is very local. (My electrodes have<br>32 channels separated by 20-200 ?m. The LFP is very very similar across<br>all the channels, so I averaged over the 32 channels to have one signal<br>for each region.)<br><br>However, I see that 2 different functions exist for the statistics :<br>FT_FREQSTATISTICS AND FT_SOURCESTATISTICS. So far, I've been using<br>ft_freqstatistics but I encounter some issues (for exemple, doing<br>monte-carlo permutation test to assess the imaginary coherence). I<br>thought of computing it manually, but I'm thinking that maybe more stuff<br>are implemented in ft_sourcestatisctics ?<br><br>? Are these 2 functions fundamentally different or do they call the same<br>sub-fonctions (and my problem has actually nothing to do with that) ?<br><br>2) I'm a bit confused with the vocabulary from EEG and MEG studies (I'm<br>not used to it yet...). From what I understood, in human studies, you<br>can do comparison for a single subject (across trials) or across<br>subjects. But I have 3 levels of comparisons in my design :<br><br>- WITHIN A SESSION, I WANT TO COMPARE ACROSS TRIALS (the 20 trials of<br>condition 1 VS the 20 trials of condition 2).<br><br>- WITHIN A RAT, I WANT TO COMPARE ACROSS SESSIONS (between the 2<br>conditions)<br><br>- then - in the very end - ACROSS RATS. But I have only 2 rats so far,<br>so I will deal with this later.<br><br>I'm a bit confused when reading the tutorials and the mailing list,<br>especially when it comes to the statistics... For example : this is from<br>an email from 2013 by Eric Maris about "Nonparametric statistical<br>testing of phase coherence"<br>(http://mailman.science.ru.nl/pipermail/fieldtrip/2013-April/006401.html)<br>"To compare coherence between conditions across subjects (instead of<br>trials), you need a different statfun: depsamplesT (for a<br>within-subjects design; subjects have participated in all conditions) or<br>indepsamplesT (for a between-subjects design; subjects have participated<br>in only one condition)."<br><br>? If I want to compare across sessions (for a same rat), can I actually<br>consider that my different sessions are "subjects"? And then compare<br>coherence "across subjects" would be doing it "across sessions" ? And I<br>would be in a "within-subject design" since my sessions involve the 2<br>conditions every time ?<br><br>I realise that it may be very confusing... I hope you will understand my<br>problem !<br><br>And if anyone already applied fieldtrip functions to do statistics on a<br>different framework that the usual EEG/MEG, please let me know !<br><br>Thanks a lot,<br><br>Laetitia Lalla<br><br>PhD Student in Neuroscience<br><br>INMED, Marseille, France<br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160408/2aed96c1/attachment-0001.html><br><br>------------------------------<br><br>_______________________________________________<br>fieldtrip mailing list<br>fieldtrip@donders.ru.nl<br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br><br>End of fieldtrip Digest, Vol 65, Issue 7<br>****************************************<br><br>_______________________________________________<br>fieldtrip mailing list<br>fieldtrip@donders.ru.nl<br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br></div></blockquote></div><br></div></body></html>