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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks Martin and Eric,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I have not tried using some of these options (for instance subdivided octahedrons) so will play around with some of these further. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Neither have I been using cortical patch information – so I will try and get to grips with this as well.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for your help, much appreciated,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Andy<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><a name="_MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></a></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Eric Larson [mailto:larson.eric.d@gmail.com] <br><b>Sent:</b> 11 November 2013 19:23<br><b>To:</b> Martin Luessi<br><b>Cc:</b> acgt2@cam.ac.uk; mne_analysis@nmr.mgh.harvard.edu<br><b>Subject:</b> Re: [Mne_analysis] Displaying .stc data as discreet 'hexagons' of colour on the freesurfer-generated mesh<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hey Andy,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The underlying source space definitions use triangulations -- you could try looking at `use_tris` for `ico` or `oct` source spaces. I /think/ that would give you triangulations with 10242 vertices (for ico-5 at least) that you could plot directly with OpenGL. In any case, the ico and oct source space generation code is now available in mne-python, so you might want to take a look at how that works to see if it otherwise contains the information you need.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Eric<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Nov 11, 2013 at 5:27 AM, Martin Luessi <<a href="mailto:mluessi@nmr.mgh.harvard.edu" target="_blank">mluessi@nmr.mgh.harvard.edu</a>> wrote:<o:p></o:p></p><p class=MsoNormal>Hi Andy,<br><br>Let me try to answer some of your questions. The problem is that the<br>source space with 10242 sources (ico-5) is created by using a subset of<br>the vertices in the full resolution FreeSurfer (FS) mesh but the number<br>of vertices in the FS mesh is subject specific. So, naturally you won't<br>get nice hexagons, as the number of vertices is not a multiple of 10242.<br><br>If you want to show patches, the "--cps" option when using<br>mne_setup_source_space. This will include a<br>"FIFF_MNE_SOURCE_SPACE_NEAREST" tag in created fiff file, which gives<br>you the closest (geodesic dist.) vertex in the 10242 mesh for every<br>vertex in the FS mesh. So you could use this information to create your<br>patches (which won't be exactly hexagonal). In the Python code, relevant<br>lines are:<br><br>a) Reading nearest from fiff file:<br><br><a href="https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py#L375" target="_blank">https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py#L375</a><br><br>b) Converting nearest to patches (list of neighbors in FS mesh for every<br>vertex in the 10242 mesh):<br><br><a href="https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py#L88" target="_blank">https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py#L88</a><br><br>I hope this helps.<br><br>Martin<o:p></o:p></p><div><p class=MsoNormal><br><br>On 11/11/13 07:57, <a href="mailto:acgt2@cam.ac.uk">acgt2@cam.ac.uk</a> wrote:<br>> Hi MNE mailing-list,<br>><br>> I am trying to display my .stc data (downsampled to 10242 sources) as<br>> discreet ‘hexagons’ of colour on the freesurfer-generated mesh, with<br>> sharp boundaries (ie no interpolation), between each hexagon.<br>><br>> (I am not doing this colouring using any of the MNE visualisation tools,<br>> instead rendering the mesh and colouring vertices/faces using openGL)<br>><br>> Unfortunately, although the ‘data-bearing’ vertices are at the centre of<br>> ‘notional’ tessellating hexagons, these hexagons are not exactly<br>> divisible by faces (see attached – white is the actual mesh, black the<br>> ‘notional’ hexagons, and ‘D’ represents the data bearing vertices<br>> present in the .stc file). You can see that I have problems in the<br>> corners of each of the ‘notional’ hexagons, as the black and white lines<br>> don’t match.<br>><br>> So a couple of questions:<br>><br>> I’m guessing that this was the reason to use smoothing/blurring in<o:p></o:p></p></div><p class=MsoNormal>> MNE_analyse (chapter 8.3of the manual) rather than simply having<o:p></o:p></p><div><p class=MsoNormal>> discreet hexagonal patches, in as much that set at the right level, the<br>> resultant colouring will always begin to approximate hexagons? Second,<br>> is this mismatch between the notional hexagon and mesh faces true for<br>> all resolutions (I’m pretty sure it is, but just want to check)? And<br>> lastly - has anyone else wanted to display these discreet ‘notional’<br>> hexagons and thought of a work-around?<br>><br>> Thanks in advance for any thoughts,<br>><br>> Andy<br>><br>><br>><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>> _______________________________________________<br>> Mne_analysis mailing list<br>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>><br><br><br>--<br>Martin Luessi, Ph.D.<br><br>Research Fellow<br><br>Department of Radiology<br>Athinoula A. Martinos Center for Biomedical Imaging<br>Massachusetts General Hospital<br>Harvard Medical School<br>149 13th Street<br>Charlestown, MA 02129<br><br>Fax: <a href="tel:%2B1%20617%20726-7422">+1 617 726-7422</a><br>_______________________________________________<br>Mne_analysis mailing list<br><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br><br><br>The information in this e-mail is intended only for the person to whom it is<br>addressed. If you believe this e-mail was sent to you in error and the e-mail<br>contains patient information, please contact the Partners Compliance HelpLine at<br><a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>but does not contain patient information, please contact the sender and properly<br>dispose of the e-mail.<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>