<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="NL-BE" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I’ve estimated the sources of two conditions using individual MRIs with warped grid from a template (1cm spacing). I ran a cluster-based permutation to find the significant voxels and I’m choosing the voxel where the
difference is bigger. I’ve had some problems defining what that voxel is. I’ve used two options: giving the position to the atlas_lookup function, and giving the index to an interpolated tissue matrix from an atlas. Given that grid occupies the brain volume
(in the BEM model with 3 layers), I also created a mask to restrict the voxels of interest to the cortex from the atlas. I seem to get different results with these and I don’t understand why. All matrices are in cm. This is part of the code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Note: The variables are<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">atlas = ft_read_atlas(‘…\fieldtrip-20141023\template\atlas\aal\ROI_MNI_V4.nii'); % then converted to ‘cm’<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">sourcemodel = grid with 1cm spacing from template<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">stat = structure from ft_sourcestatistics<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Create mask from atlas<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg = []; <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.interpmethod = 'nearest'; <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.parameter = 'tissue'; <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">sourcemodel2 = ft_sourceinterpolate(cfg,atlas,sourcemodel);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">atlas_one= sourcemodel2.tissue > 0; % Logical matrix with points with an anatomical label<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 1)Look for labels with atlas mask<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[val ind_max] = max(stat.stat(:).* atlas_one(:));<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 1.a)--------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Atlas_lookup<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">pos = stat.pos(ind_max,:);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">atlas_lookup(atlas, pos, 'inputcoord', 'mni')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Results<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% MNI coordinates: 4 -1 2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Label: Rolandic_Oper_R<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 1.b)--------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Interpolated tissue from atlas<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[xi yi zi] = ind2sub(stat.dim, ind_max);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">atlas.tissuelabel{sourcemodel2.tissue(xi, yi, zi)}<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Results<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Voxel coordinates: 12 10 10<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Label: Rolandic_Oper_R<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 2)Look for labels without atlas mask<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[val ind_max] = max(stat.stat(:));<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 2.a)--------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Atlas_lookup<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Results<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% MNI coordinates: 4 -1 3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Label: Postcentral_R<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% 2.b)--------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Interpolated tissue from atlas<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Results<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">% Voxel coordinates: 12 10 11<o:p></o:p></span></p>
<p class="MsoNormal">% Label: None<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">What is it that I’m missing?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you in advance for any help!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><b><span lang="EN-US" style="font-size:11.5pt;color:#1D8DB0;mso-fareast-language:NL-BE">Laura Rueda Delgado</span></b><span lang="EN-US" style="font-size:11.5pt;color:#333333;mso-fareast-language:NL-BE"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span lang="EN-US" style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">PhD student<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span lang="EN-US" style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">Department of Kinesiology- Motor Control and Neural Plasticity Research Group<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">KU Leuven<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">Tervuursevest 101 bus 1501<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">3001 Leuven, Belgium<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;background:white"><span style="font-size:9.0pt;color:#333333;mso-fareast-language:NL-BE">tel. +32 16 37 64 78</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#333333;mso-fareast-language:NL-BE"><br>
<br>
</span><span style="mso-fareast-language:NL-BE"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>