<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Hi Gus,<div><br><div><div>On Dec 3, 2009, at 11:31 AM, Gustavo Sudre wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello all,<br><br>Thank you again for the good discussing on that previous issue. Now I <br>have a more MNE-specific question.<br><br>Suppose I run compute_mne_raw_inverse using a single label (e.g. <br>cortex-lh.label), and then convert the output of that function to <br>a .mat file using mne_raw2mat. </div></blockquote><div><br></div><div>First, the use of mne_raw2mat is quite unnecessary. You can read the signals directly from the fif files with the Matlab routines. This saves time and disk space. A good starting point is mne_ex_read_raw.</div><div><br></div><blockquote type="cite"><div>In the resulting .mat file I see a <br>[channels] by [time] matrix with data, which makes sense. Judging by <br>the number of channels, I imagine they map to the sources within that <br>label, and not the vertices. Then, in the info structure there are <br>names for all these channels, and if I understand it correctly that <br>contains the number of the vertex that the source maps to. In that <br>case, is there a 1-1 relationship between sources and vertices? That <br>would mean that there's an awful lot of quiet voxels in the results <br>(e.g. given the ~3000 sources I get in the left hemisphere, using 7mm <br>spacing, and 160K vertices being indexed). Shouldn't a given source <br>affect more than one vertex in the brain, if the triangles are small <br>enough?<br><br>I guess my question boils down to the definition and relationship <br>between vertices and sources. Please let me know if I'm mistaken in my <br>line of thought.<br></div></blockquote><div><br></div>Anyhow, in the info structure contained in the mat file output by mne_raw2mat there is a field ch_lognos which contains the vertex numbers of the sources in the densely triangulated surface. There is the logno field in the channel descriptors if you load the fif file directly.</div><div><br></div><div>For visualization and morphing MNE uses a "spreading operator" to fill in values to all vertices. This is discussed in section 8.3 of the MNE manual.</div><div><br></div><div>- Matti</div><div><br></div><div><br></div></div><br><br><div apple-content-edited="true"> <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; "><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; "><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"></div></span><br class="Apple-interchange-newline"> </div><br></body></html>