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<p style="margin-bottom:0in;line-height:100%">Pipeline for
sourceanalysis with individualize grip</p>
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<p style="margin-bottom:0in;line-height:100%">
</p><p style="margin-bottom:0in;line-height:100%">Dear field trippers,</p>
<p style="margin-bottom:0in;line-height:100%"><br>
</p>
<p style="margin-bottom:0in;line-height:100%">I have a question
related to pipeline for sourceanalysis with individualize grid.</p>
<p style="margin-bottom:0in;line-height:100%">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%">Best Regards,</p>
<p style="margin-bottom:0in;line-height:100%">Olga.</p>
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<p style="margin-bottom:0in;line-height:100%">% 1. load template
grid, e.g.
</p>
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<p style="margin-bottom:0in;line-height:100%"><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">load(</font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'/net/server/mnt/programs/olgas/fieldtrip-20160119/template/sourcemodel/standard_sourcemodel3d10mm.mat'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">);</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">template_grid
= sourcemodel;</font></font></font></p>
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</p>
<p style="margin-bottom:0in;line-height:100%"><a name="make_the_individual_subjects_grid"></a>
<font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">%2.
</font></font></font>Make the individual subjects' grid</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">%a)
Load individual subject mri, e.g.</font></font></font></p>
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</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">[mri{Subj_i}]
= ft_read_mri(path_MRI{Subj_i});</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">mri_cm{Subj_i}
= ft_convert_units(mri{Subj_i}, 'cm');</font></font></font></p>
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</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">%</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">b)</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">
construct individual grid by projecting to template grid</font></font></font></p>
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</font><br>
</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg
= [];</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grid.warpmni
= 'yes';</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grid.template
= template_grid;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grid.nonlinear
= 'yes'; % use non-linear normalization</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.mri
= mri_cm{Subj_i};</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">grid_ind{Subj_i}
= ft_prepare_sourcemodel(cfg);</font></font></font></p>
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</p>
<p style="margin-bottom:0in;line-height:100%">% 3. Make source reconstruction, using individualized grid and<b> template? or individual
headmodel</b></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">%</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">a)
load template volume</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">
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%"><font color="#228b22">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">template_vol
= vol;</font></font></font></p>
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</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg
= [];</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grid
= grid_ind{Subj_i};</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
</font><font color="#000000"> <font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>cfg.vol
= vol_K0012_cm; </b></font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>%
</b></font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>individual</b></font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>
</b></font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>or
template </b></font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>vol???</b></font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.channel
= {</font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'MEG'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">};</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grad
= freq_cmb{Subj_i}.grad;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">sourcemodel_lf_K0012
= ft_prepare_leadfield(cfg, freq_cmb{Subj_i});</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
</font><br>
</p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg
= [];</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.frequency
= freq_cmb{Subj_i}.freq;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.grad
= freq_cmb{Subj_i}.grad;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.method
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'dics'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.keeptrials
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'yes'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
</font><font color="#000000"> <font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>cfg.grid
= sourcemodel_lf{Subj_i}; % </b></font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2"><b>sourcemodel
after leadfield with individual or template headmodel?</b></font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<b><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.vol
= vol_K0012_cm; </font></font></b></font><b><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">%
</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">individual</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">
</font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">or
template </font></font></font><font color="#228b22"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">vol???</font></font></font></b></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.keeptrials
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'yes'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.dics.lambda
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'5%'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.dics.keepfilter
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'yes'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.dics.fixedori
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'yes'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">cfg.dics.realfilter
= </font></font></font><font color="#a020f0"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">'yes'</font></font></font><font color="#000000"><font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">;</font></font></font></p>
<p style="margin-bottom:0in;line-height:100%"><font color="#000000">
<font face="lucidatypewriter, serif"><font style="font-size:10pt" size="2">source_K0012
= ft_sourceanalysis(cfg, freq_cmb{Subj_i});</font></font></font></p>
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</p>
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