<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style id="owaParaStyle">P {
MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
P {
MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px
}
</style>
</head>
<body fPStyle="1" ocsi="0">
<div style="FONT-FAMILY: Tahoma; DIRECTION: ltr; COLOR: #000000; FONT-SIZE: 10pt">
<p>Deal Alex,</p>
<p> </p>
<p>Thank you so much for the quick reply, I managed to do what you suggested then got stuck at loading the '_sm_flip.tri' files to MATLAB<a></a>.</p>
<p> </p>
<p>This may be a very naive question, but hope you can give me some help on this please.</p>
<p> </p>
<p>Many thanks</p>
<p> </p>
<p>Kind regards</p>
<p><a></a>Imali </p>
<div style="FONT-FAMILY: Times New Roman; COLOR: #000000; FONT-SIZE: 16px">
<hr tabindex="-1">
<div style="DIRECTION: ltr" id="divRpF16672"><font color="#000000" size="2" face="Tahoma"><b>From:</b> alexandre.gramfort@gmail.com [alexandre.gramfort@gmail.com<a></a>] on behalf of Alexandre<a></a> Gramfort<a></a> [alexandre.gramfort@inria.fr<a></a>]<br>
<b>Sent:</b> Tuesday, 12 June 2012 4:10 PM<br>
<b>To:</b> FieldTrip<a></a> discussion list; IMALI<a></a> THANUJA<a></a> HETTIARACHCHI<a></a><br>
<b>Subject:</b> Re: [FieldTrip<a></a>] Headmodel<a></a> with NeuroScan<a></a> meshes<br>
</font><br>
</div>
<div></div>
<div>hi <span style="BORDER-COLLAPSE: collapse; FONT-FAMILY: Tahoma,sans-serif; COLOR: rgb(34,34,34); FONT-SIZE: 13px" class="Apple-style-span"><span style="BORDER-COLLAPSE: collapse; FONT-FAMILY: Tahoma,sans-serif; COLOR: rgb(34,34,34); FONT-SIZE: 13px" class="Apple-style-span">Imali</span><a></a>,</span>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span"><br>
</span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span">your meshes had indeed tiny problems. To fixed it I just smoothed a tiny bit the meshes.</span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span"><br>
</span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span">In matlab<a></a>:</span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span"><br>
</span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span">>> load innerSkull<a></a></span></font></div>
<div><font class="Apple-style-span" color="#222222" face="Tahoma, sans-serif"><span style="BORDER-COLLAPSE: collapse" class="Apple-style-span">>> om_save_tri<a></a>('innerSkull.tri<a></a>', curryloc<a></a>', currytri<a></a>');</span></font></div>
<div><br>
</div>
<div>then :</div>
<div><br>
</div>
<div>$om_mesh_smooth<a></a> -i<a></a> innerSkull.tri<a></a> -o innerSkull_sm.tri<a></a> -n 2</div>
<div>$om_mesh_convert<a></a> -i<a></a> innerSkull_sm.tri<a></a> -o innerSkull_sm_flip.tri<a></a> -invert</div>
<div>
<div>$ om_mesh_info<a></a> -i<a></a> innerSkull_sm_flip.tri<a></a> </div>
<div><a></a>om_mesh_info version 2.2.dev<a></a> (exported) compiled at Mar 7 2012 15:37:20</div>
<div><br>
</div>
<div><a></a>load_tri : innerSkull_sm_flip.tri<a></a></div>
<div>Mesh Info : </div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span># points : 2934</div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span># triangles : 5864</div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>Euler characteristic : 2</div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>Min Area : 6.55783</div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>Max Area : 28.9211</div>
<div>Mesh orientation correct (valid for closed mesh).</div>
<div><br>
</div>
<div>this should fix the problem. Note that you can surely also smooth the meshes in matlab<a></a>.</div>
<div><br>
</div>
<div>Alex</div>
<div>
<div>-- </div>
<div><a></a>Alexandre Gramfort<a></a>, PhD</div>
<div><a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a><a></a><a href="mailto:alexandre.gramfort@inria.fr" target="_blank"></a></div>
<div><a></a>INRIA Parietal Project Team, NeuroSpin<a></a> CEA<a></a> Saclay<a></a></div>
<div>Bat. 145, PC 156</div>
<div>91191 Gif-sur<a></a>-Yvette, France</div>
<div><a href="http://alexandre.gramfort.net" target="_blank">http://alexandre.gramfort.net</a></div>
</div>
<div><br>
</div>
<div class="gmail_quote">On Tue, Jun 12, 2012 at 3:25 AM, IMALI<a></a> THANUJA<a></a> HETTIARACHCHI<a></a>
<span dir="ltr"><<a href="mailto:ith@deakin.edu.au" target="_blank">ith@deakin.edu.au</a><a></a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div lang="EN-AU">
<div>
<p class="MsoNormal"><u></u><u></u> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">Dear FieldTrip<a></a> users,<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">As I have faced problems in creating a head model with MRI's, so I thought to try the MNI<a></a> head for creating the meshes. I used the NeuroScan<a></a> software to create the surface meshes
and exported them to Matlab<a></a>. Then tried to crate the head model using ft_prepare_headmodel<a></a> function. however the 'om_minverser<a></a>' stops working and the program terminates.<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">When I plot the meshes they seem fine to me so I assume that there is no segmenting issues. But Now I get an error as attached in the 'log.txt<a></a>' from the Matlab<a></a> workspace, which
says about self intersecting meshes. I have attached the Neuroscan<a></a> exported meshes (innerSkull.mat,outerSkull.mat,skin.mat<a></a>) and the Matlab<a></a> function (m_file.txt<a></a>) that I used in creating the head model.<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">I really want to generate some simulated EEG data but cannot make anything work. If someone can give a guidance on where I am going wrong in the procedure , that will be highly appreciated.<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">Many thanks.<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">Kind regards<u></u><u></u></span></p>
<p><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><a></a><u></u><u><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt">Imali</span></u></span></p>
<p class="MsoNormal"><u></u><u></u> </p>
<p class="MsoNormal"><b><span style="FONT-FAMILY: 'Times New Roman','serif'"><a></a><b><span style="FONT-FAMILY: 'Times New Roman','serif'">Imali</span></b> Thanuja<a></a> Hettiarachchi<a></a><u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'">PhD Candidate<u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'">Centre for Intelligent Systems research<u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'">Deakin University,
</span><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt">Geelong 3217, Australia.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt">Mobile :
<a href="tel:%2B61430321972" target="_blank" value="+61430321972">+61430321972</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt">Email:
<span style="COLOR: blue"><a href="mailto:ith@deakin.edu.au" target="_blank"><span style="COLOR: blue">ith@deakin.edu.au</span></a><a></a></span><br>
</span><span style="FONT-FAMILY: 'Times New Roman','serif'"><a href="http://www.deakin.edu.au/cisr" target="_blank"><span style="COLOR: blue">www.deakin.edu.au/cisr</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'"><u></u><u></u></span> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Helvetica','sans-serif'; FONT-SIZE: 9pt"><img border="0" alt="Description: Description: Description: cid:1216BE20-1800-4A47-8B9F-E7B9D94831CD@deakin.edu.au" width="70" height="73"><span style="WIDTH: 0px; HEIGHT: 0px; OVERFLOW: hidden" id="OWAImgPlaceHolder"> </span></span><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><u></u><u></u></span> </p>
<p class="MsoNormal"><span style="FONT-FAMILY: 'Tahoma','sans-serif'; FONT-SIZE: 10pt"><br>
<br>
</span><span><u></u><u></u></span></p>
<p class="MsoNormal"><u></u><u></u> </p>
</div>
</div>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>
<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<a></a> 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.<br>
<br>
</blockquote>
</div>
<br>
<div name="mailplane_signature">
<div>-- <br>
Alexandre<a></a> Gramfort<a></a>, PhD<br>
<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a><a></a><br>
INRIA<a></a> Parietal Project Team @ NeuroSpin<a></a> CEA<a></a> Saclay<a></a><br>
Bat. 145, PC 156<br>
91191 Gif-sur<a></a>-Yvette, France<br>
<a href="http://www-sop.inria.fr/members/Alexandre.Gramfort/" target="_blank">http://www-sop.inria.fr/members/Alexandre.Gramfort/</a>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>