<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Olga,<div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><p class="" style="margin-bottom: 0in; line-height: 12px;">Should I use template or subject-specific headmodel with “projected to template grid individualized grid”?</p></div></blockquote></div><div class=""><br class=""></div><div class="">I would use the individual head model based on the MRI as it provides more information for your source analysis. This should provide more accurate results.</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><p class="" style="margin-bottom: 0in; line-height: 12px;">Actually I tried both ways for one subject and did not notice any difference in the results. </p></div></blockquote></div><div class=""><br class=""></div><div class="">It seems to that this is due to this line of code, but I’m not quite sure about that:</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">cfg = [];</font></font></font></p><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">cfg.grid.warpmni = 'yes';</font></font></font></p><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">cfg.grid.template = template_grid;</font></font></font></p><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">cfg.grid.nonlinear = 'yes'; % use non-linear normalization</font></font></font></p><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">cfg.mri = mri_cm{Subj_i};</font></font></font></p><p class="" style="margin-bottom: 0in; line-height: 12px;"><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font class="" style="font-size: 10pt;">grid_ind{Subj_i} = ft_prepare_sourcemodel(cfg);</font></font></font></p></div></blockquote></div><div class=""><br class=""></div><div class="">I think with this configuration the source model that is prepared is only based on the cfg.grid.template, and completely ignores the MRI (which you are interested in). This might explain why you see no difference.</div><div class=""><br class=""></div><div class="">Bests,</div><div class=""><br class=""><div class="">
Simon Homölle<br class="">PhD Candidate<br class="">Donders Institute for Brain, Cognition and Behaviour<br class="">Centre for Cognitive Neuroimaging<br class="">Radboud University Nijmegen<br class="">Phone: +31-(0)24-36-65059
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 09 Mar 2016, at 11:57, Olga Sysoeva <<a href="mailto:olga.v.sysoeva@gmail.com" class="">olga.v.sysoeva@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><p style="margin-bottom:0in;line-height:100%" class="">Pipeline for
sourceanalysis with individualize grip</p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><div style="margin-bottom: 0in; line-height: 100%;" class="">
<br class="webkit-block-placeholder"></div><p style="margin-bottom:0in;line-height:100%" class="">Dear field trippers,</p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class="">I have a question
related to pipeline for sourceanalysis with individualize grid.</p><p style="margin-bottom:0in;line-height:100%" class="">Should I use
template or subject-specific headmodel with “projected to template
grid individualized grid”? Below is my pipeline with details of
what I mean. Actually I tried both ways for one subject and did not
notice any difference in the results. Does it mean that I do not need
to constract headmodel for each subject? That's indeed save a lot of
time, but I'd like to get your green light on this.</p><p style="margin-bottom:0in;line-height:100%" class="">Best Regards,</p><p style="margin-bottom:0in;line-height:100%" class="">Olga.</p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class="">% 1. load template
grid, e.g.
</p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">load(</font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'/net/server/mnt/programs/olgas/fieldtrip-20160119/template/sourcemodel/standard_sourcemodel3d10mm.mat'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">);</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">template_grid
= sourcemodel;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><a name="make_the_individual_subjects_grid" class=""></a>
<font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">%2.
</font></font></font>Make the individual subjects' grid</p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">%a)
Load individual subject mri, e.g.</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">[mri{Subj_i}]
= ft_read_mri(path_MRI{Subj_i});</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">mri_cm{Subj_i}
= ft_convert_units(mri{Subj_i}, 'cm');</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">%</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">b)</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">
construct individual grid by projecting to template grid</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class="">
</font><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg
= [];</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grid.warpmni
= 'yes';</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grid.template
= template_grid;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grid.nonlinear
= 'yes'; % use non-linear normalization</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.mri
= mri_cm{Subj_i};</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">grid_ind{Subj_i}
= ft_prepare_sourcemodel(cfg);</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class="">% 3. Make source reconstruction, using individualized grid and<b class=""> template? or individual
headmodel</b></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">%</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">a)
load template volume</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">
load('/net/server/data/programs/olgas/fieldtrip-20160119/template/headmodel/standard_singleshell.mat');</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font color="#228b22" class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">template_vol
= vol;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg
= [];</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grid
= grid_ind{Subj_i};</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
</font><font class=""> <font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">cfg.vol
= vol_K0012_cm; </b></font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">%
</b></font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">individual</b></font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">
</b></font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">or
template </b></font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">vol???</b></font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.channel
= {</font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'MEG'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">};</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grad
= freq_cmb{Subj_i}.grad;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">sourcemodel_lf_K0012
= ft_prepare_leadfield(cfg, freq_cmb{Subj_i});</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
</font><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg
= [];</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.frequency
= freq_cmb{Subj_i}.freq;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.grad
= freq_cmb{Subj_i}.grad;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.method
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'dics'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.keeptrials
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'yes'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
</font><font class=""> <font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">cfg.grid
= sourcemodel_lf{Subj_i}; % </b></font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class=""><b class="">sourcemodel
after leadfield with individual or template headmodel?</b></font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<b class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.vol
= vol_K0012_cm; </font></font></b></font><b class=""><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">%
</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">individual</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">
</font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">or
template </font></font></font><font color="#228b22" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">vol???</font></font></font></b></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.keeptrials
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'yes'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.dics.lambda
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'5%'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.dics.keepfilter
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'yes'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.dics.fixedori
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'yes'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">cfg.dics.realfilter
= </font></font></font><font color="#a020f0" class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">'yes'</font></font></font><font class=""><font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">;</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><font class="">
<font face="lucidatypewriter, serif" class=""><font style="font-size:10pt" size="2" class="">source_K0012
= ft_sourceanalysis(cfg, freq_cmb{Subj_i});</font></font></font></p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p><p style="margin-bottom:0in;line-height:100%" class=""><br class="">
</p>
</div>
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