<html><head><base href="x-msg://8/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Tyler,<div><br></div><div>if you follow the link, you get to the "Volumes of Interest" Data base.</div><div>You can browse through the volumes by then clicking on "Alphabetic index" (<a href="http://neuro.imm.dtu.dk/services/jerne/ninf/voi/index-alphabetic.html">http://neuro.imm.dtu.dk/services/jerne/ninf/voi/index-alphabetic.html</a>)</div><div>If you then click on a volume (e.g. "amygdala" <a href="http://neuro.imm.dtu.dk/services/jerne/ninf/voi/amygdala.html">http://neuro.imm.dtu.dk/services/jerne/ninf/voi/amygdala.html</a>) you get to a definition of that VOI. Here, you can now download .hdr and .img files. These are ANALYZE volumes with 1s for all voxels inside a VOI and 0s outside.</div><div>You can read these with ft_read_mri and normalize to the MNI brain.</div><div><br></div><div>tl;dr You don't need any functions, just the .hdr and .img files defining the volumes</div><div><br></div><div>Best,</div><div><br></div><div>Julian</div><div><br><div><div>Am 28.05.2014 um 03:06 schrieb Tyler Grummett:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; 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 dir="ltr"><div id="OWAFontStyleDivID" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif; "><div style="margin-top: 0px; margin-bottom: 0px; ">Hey Julian,<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it?<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Regards,<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Tyler<br></div><div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-size: 13px; ">*************************<div style="font-family: Tahoma; "><br></div><div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div><div><font face="Arial"><i>PhD Candidate</i></font></div><div><font face="Arial"><i>Brain Signals Laboratory</i></font></div><div><font face="Arial"><i>Flinders University</i></font></div><div><font face="Arial"><i>Rm 5A301</i></font></div><div><font face="Arial"><i>Ext 66124</i></font></div></div></div></div></div></div></div><div style="color: rgb(40, 40, 40); "><hr tabindex="-1" style="display: inline-block; width: 717px; "><div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size: 11pt; "><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a><span class="Apple-converted-space"> </span><<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>> on behalf of Julian Keil <<a href="mailto:julian.keil@gmail.com">julian.keil@gmail.com</a>><br><b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, 28 May 2014 1:55 AM<br><b>To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] granger causality on beamformer data</font><div> </div></div><div><div dir="ltr"><div><div><div><div><div>Hi Tyler,<br><br></div>I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400<span class="Apple-converted-space"> </span><br>connections, so I hope you have a fast computer.<br><br></div>As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:<a href="http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html">http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html</a><br><br></div><div>The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI.<br></div><div><br></div>In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI).<br><br>I hope that helps, if you have specific questions, feel free to ask.<br><br></div>Best,<br><br></div>Julian<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:tyler.grummett@flinders.edu.au" target="_blank">tyler.grummett@flinders.edu.au</a>></span><span class="Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; "><div dir="ltr"><div style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif; "><div style="margin-top: 0px; margin-bottom: 0px; ">Hello fieldtrippers,<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Or should you do a PCA reduction of some description beforehand.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Im open to all suggestions.<br></div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div style="margin-top: 0px; margin-bottom: 0px; ">Tyler<br></div><div><div style="margin-top: 0px; margin-bottom: 0px; "><br></div><div name="divtagdefaultwrapper"><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-size: 13px; ">*************************<div style="font-family: Tahoma; "><br></div><div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div><div><font face="Arial"><i>PhD Candidate</i></font></div><div><font face="Arial"><i>Brain Signals Laboratory</i></font></div><div><font face="Arial"><i>Flinders University</i></font></div><div><font face="Arial"><i>Rm 5A301</i></font></div><div><font face="Arial"><i>Ext 66124</i></font></div></div></div></div></div></div></div></div></div><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br></div></div></div></div>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div></span></blockquote></div><br></div></body></html>