<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Hi Tim,<div><br><div><div><div>On May 16, 2011, at 2:42 PM, Bardouille, Tim wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Thanks for your prompt replies.<br><br>The problem that I'm encountering is knowing which vertices on the fsaverage anatomical surface correspond to the 10242 vertices in the functional .stc data. Mne_analyze reports an anatomical vertex number based on the fsaverage surface from 1 to ~125,000, while the functional data has only 10242 vertices.<br><br>Example: If I load the .stc file into mne_analyze on the fsaverage brain, then see some activation, I want to go back now and know to which of the 10242 time courses it relates. <br><br>So what I'm looking for is the mapping between the 10242 functional vertices in my .stc file and the anatomical vertices on the fsaverage surface.<br><br>I hope this makes my question more clear.<br></div></blockquote><div><br></div><div>When you have morphed the data to fsaverage with the standard settings, the output stc files contain 10242 vertices, which is a sparse sample of the about 125000 vertices in an fsaverage hemisphere. Because of the way that the fsaverage surfaces have been constructed, these 10242 vertices are also the first 10242 vertices in the fsaverage tessellation. Generally, the vertex numbers do not bear any spatial information with them as such. This is particularly true with the fsaverage brain. Forexample, vertices 1,2, and 3 are nowhere near vertex 0 on the cortical surface. The vertex closest to vertex 0 is far down the line in the vertex list. </div><div><br></div><div><br></div>I hope this helps,</div><div>Matti</div><div><br></div><div><br><blockquote type="cite"><div><br>Best,<br>Tim.<br><br>---------------------------------------------------------<br>Timothy Bardouille, PhD, Research Officer<br>Laboratory for Clinical MEG<br>NRC Institute for Biodiagnostics (Atlantic)<br>Office: Halifax Infirmary<br>3900 - 1796 Summer Street<br>Halifax, Nova Scotia B3H 3A7<br>Phone: 902-473-1865<br>Lab: 902-470-3936<br>Fax: 902-473-1851<br>---------------------------------------------------------<br>________________________________________<br>From: <a href="mailto:sheraz@nmr.mgh.harvard.edu">sheraz@nmr.mgh.harvard.edu</a> [sheraz@nmr.mgh.harvard.edu]<br>Sent: May 16, 2011 2:30 PM<br>To: Bardouille, Tim<br>Cc: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu">mne_analysis@nmr.mgh.harvard.edu</a><br>Subject: Re: [Mne_analysis] Vertex mapping for fsaverage<br><br>Hi Tim,<br><br>There is vertices field inside stc structure if you open it in Matlab.<br>Just add 1 to it, it will correspond to vertices on fsaverage brain.<br><br><br>stc = mne_read_stc_file(stcfile);<br>fsAverageVertices=1+squeeze(stc.vertices(:,1));<br><br><br><br>Regards<br><br>Sheraz<br><br><br><br><blockquote type="cite">Hi there,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Sorry if this question has already been answered. If so, please point me<br></blockquote><blockquote type="cite">to the appropriate thread.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am doing some group stats analysis on my dSPM .stc maps after morping to<br></blockquote><blockquote type="cite">the fsaverage space. When I load the morphes .stc maps into Matlab I have<br></blockquote><blockquote type="cite">10242 vertices per hemisphere, but the structure that is generated by<br></blockquote><blockquote type="cite">mne_read_stc_file does not indicate (for each vertex) which is the<br></blockquote><blockquote type="cite">corresponding vertex on the fsaverage anatomical surface. This information<br></blockquote><blockquote type="cite">must be somewhere, however, as I can view the .stc maps on the fsaverage<br></blockquote><blockquote type="cite">brain in mne_analyze.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I'd like to get access to this mapping to help me interpret the results.<br></blockquote><blockquote type="cite">Is there a way to access this information?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Tim.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">---------------------------------------------------------<br></blockquote><blockquote type="cite">Timothy Bardouille, PhD, Research Officer<br></blockquote><blockquote type="cite">Laboratory for Clinical MEG<br></blockquote><blockquote type="cite">NRC Institute for Biodiagnostics (Atlantic)<br></blockquote><blockquote type="cite">Office: Halifax Infirmary<br></blockquote><blockquote type="cite">3900 - 1796 Summer Street<br></blockquote><blockquote type="cite">Halifax, Nova Scotia B3H 3A7<br></blockquote><blockquote type="cite">Phone: 902-473-1865<br></blockquote><blockquote type="cite">Lab: 902-470-3936<br></blockquote><blockquote type="cite">Fax: 902-473-1851<br></blockquote><blockquote type="cite">---------------------------------------------------------<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Mne_analysis mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br></blockquote><blockquote type="cite"><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br></blockquote><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">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.<br>_______________________________________________<br>Mne_analysis mailing list<br><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis<br><br><br></div></blockquote></div><br></div></div><br><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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>---------</div><div><br></div><div>Matti Hamalainen, Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Athinoula A. Martinos Center for Biomedical Imaging</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Massachusetts General Hospital</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></div><div><a href="mailto:msh@nmr.mgh.harvard.edu">msh@nmr.mgh.harvard.edu</a></div><div><br></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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