<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Caro Andrea,<div><br></div><div>You might want to use ft_plot_topo3d for this purpose. This will plot the functional data onto the positions of the channels in 3D, but you need to create the to-be-plotted data as a single vector, and you will need the channel positions in 3D (which you'll get for free when working with MEG data, but which are generally not represented in EEG data). If you concurrently have a cortical reconstruction defined in the same coordinate system as the channels (and in the same metric units (otherwise use ft_convert_units first)), you can do a 'hold on' and use ft_plot_mesh for the visualization of the cortex. I guess that the ft_plot_topo3D has some functionality for transparency.</div><div><br></div><div>Ciao,</div><div><br></div><div>JM</div><div><br></div><div><br></div><div><br><div><div>On Jun 20, 2012, at 8:44 PM, andrea brovelli wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Otherwise, to make things easier: is there a simple way to visualise a given topography in 3D (rather than in a 2D layout as done with ft_topoplotTFR) together with different segmented surfaces such as the skin or the brain meshes ?<br><br>Thanks<br><br>Andrea<br><br><br>----- Messaggio da <a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a> ---------<br> Data: Wed, 20 Jun 2012 18:56:58 +0200<br> Da: andrea brovelli <<a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a>><br>Rispondi-A: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br> Oggetto: Re: [FieldTrip] Projection from sensors space to segmented brain surface<br> A: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><br><br><blockquote type="cite">Thank you very much for your quick reply, Eelke and Johanna.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Yes, I would like only to visualise the data on a cortical surface and I am aware of the potential misinterpretation of such visualisation.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I would like to use it as an intermediate step between the ft_topoplot on 2D layout and proper source localisation. It would serve as an exploratory tool to decide at which frequency, say, I would do a beamforming and to have a very rough idea of the number and location of cortical sources.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">However, it is not very clear to me how I could do this using the example in the beamforming tutorial. Could you be a bit more explicit ? Should I need to do source reconstruction for visualisation ?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks a lot<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Andrea<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">----- Messaggio da <a href="mailto:johanna.zumer@donders.ru.nl">johanna.zumer@donders.ru.nl</a> ---------<br></blockquote><blockquote type="cite"> Data: Wed, 20 Jun 2012 18:22:48 +0200<br></blockquote><blockquote type="cite"> Da: Johanna Zumer <<a href="mailto:johanna.zumer@donders.ru.nl">johanna.zumer@donders.ru.nl</a>><br></blockquote><blockquote type="cite">Rispondi-A: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br></blockquote><blockquote type="cite"> Oggetto: Re: [FieldTrip] Projection from sensors space to segmented brain surface<br></blockquote><blockquote type="cite"> A: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Dear Andrea,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I would like to further clarify the options for this question. Perhaps<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">could you suggest which inverse algorithm you had in mind?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">For example, it is possible to use beamforming limited only to voxels<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">defined as lying on the cortical sheet (i.e. restrict .inside to be only<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the gray matter). This is possible, but you might miss out on the spatial<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">peak of the source lying just 5mm away to the inside a bit. Thus, it<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">would be better to do as Eelke suggested and apply beamforming to the whole<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">inside of the brain, and then project those values to the surface for<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">visualisation (which is easily done with the cfg.method='surface' option in<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ft_sourceplot).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Alternatively, you can use a min-norm type of inverse method (e.g. sLORETA<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">or MNE) which are commonly used to reconstruct onto cortical surface voxels<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">only. This works because the min-norm algorithms force all activity to lie<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">in the region over which you select to reconstruct. Thus, a source 5mm<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">inside of the surface will automatically get projected to the surface.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I also agree with Eelke you should not just project sensors to surface<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">without doing a specific type of inverse method.<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">Johanna<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2012/6/20 Eelke Spaak <<a href="mailto:eelke.spaak@donders.ru.nl">eelke.spaak@donders.ru.nl</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Andrea,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">If I understand your question correctly, you just want to *visualise*<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sensor space activity on a brain surface, without doing source<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">reconstruction first? I would advise against this. Time-frequency<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">power values of your planar gradient data reflect the spectral<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">characteristics of the magnetic gradient at the location of your<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sensors. These sensors are not located at the surface of the brain,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">but quite some centimeters away from it. Therefore, visualising the<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">data as if it were actually recorded on the brain surface, without<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">doing a proper transformation, is potentially misleading. It is true<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">that people tend to display all sorts of data in a 'topoplot' fashion,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">but in that case it is clear to the audience that you are looking at a<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">representation in sensor-space. Have a look at ft_topoplotTFR for this<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">approach, if you're not already familiar with it.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">If you want to display your time-frequency activity on a cortical<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">surface (which is of course a perfectly valid thing to want to do),<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">you first should map the sensor activity to source space. This mapping<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">is non-trivial and can be done by e.g. beamforming. See<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://fieldtrip.fcdonders.nl/tutorial/beamformer">http://fieldtrip.fcdonders.nl/tutorial/beamformer</a> for a tutorial on<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">this. That tutorial ends with a surface plot.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hope this helps!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Best,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Eelke<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On 20 June 2012 17:26, andrea brovelli <<a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a>><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Fieldtrip users and developpers,<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I would like to project and visualise time-frequency power values<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">computed<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">on planar gradient data at the sensors level onto the brain surface<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">segmentated from the anatomial MRI of the subject.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Can anyone suggest me how to do it in Fieldtrip ? Can anyone share the<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">scripts ?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Does anyone see any inconvenient to this visualisation ?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks a lot for you help.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Andrea<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> NEW EMAIL: <a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">fieldtrip mailing list<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><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></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">fieldtrip mailing list<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><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><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">----- Fine messaggio da <a href="mailto:johanna.zumer@donders.ru.nl">johanna.zumer@donders.ru.nl</a> -----<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"> NEW EMAIL: <a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a><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><br><br>----- Fine messaggio da <a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</a> -----<br><br><br>-- <br><br> NEW EMAIL: <a href="mailto:andrea.brovelli@univ-amu.fr">andrea.brovelli@univ-amu.fr</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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