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<p class="MsoNormal"
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style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US">Dear fieldtrip users,<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US">I have 2 questions
regarding the construction of grids
for individual subjects. <span style="mso-spacerun:yes"> </span><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US">This is the code I used
(the template was build according
to the tutorial “Create MNI-aligned grids…”):<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg
= [];</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:
EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.write<span
style="mso-spacerun:yes"> </span>= </span><span
style="font-size:10.0pt;font-family:"Courier
New";color:#A020F0;mso-ansi-language:
EN-US" lang="EN-US">'no'</span><span
style="font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US" lang="EN-US">;</span><span
style="font-size:
12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.coordsys<span
style="mso-spacerun:yes"> </span>= </span><span
style="font-size:
10.0pt;font-family:"Courier
New";color:#A020F0;mso-ansi-language:EN-US" lang="EN-US">'ctf'</span><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US">;</span><span
style="font-size:12.0pt;
font-family:"Courier New";mso-ansi-language:EN-US"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>[segmentedmri]
=
ft_volumesegment(cfg, mri);<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg
= [];</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:
EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.method=</span><span
style="font-size:10.0pt;font-family:"Courier
New";color:#A020F0;
mso-ansi-language:EN-US" lang="EN-US">'singleshell'</span><span
style="font-size:
10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:EN-US" lang="EN-US">;<span
style="mso-spacerun:yes"> </span></span><span
style="font-size:
10.0pt;font-family:"Courier
New";color:forestgreen;mso-ansi-language:EN-US"
lang="EN-US">%
or single sphere model</span><span style="font-size:12.0pt;
font-family:"Courier New";mso-ansi-language:EN-US"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>vol
=
ft_prepare_headmodel(cfg, segmentedmri);<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg
= [];</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:
EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.grid.warpmni<span
style="mso-spacerun:yes"> </span>= </span><span
style="font-size:
10.0pt;font-family:"Courier
New";color:#A020F0;mso-ansi-language:EN-US" lang="EN-US">'yes'</span><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US">;</span><span
style="font-size:12.0pt;
font-family:"Courier New";mso-ansi-language:EN-US"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.grid.template<span
style="mso-spacerun:yes"> </span>= template_grid;</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.grid.nonlinear
= </span><span
style="font-size:10.0pt;font-family:"Courier
New";color:#A020F0;
mso-ansi-language:EN-US" lang="EN-US">'yes'</span><span
style="font-size:10.0pt;
font-family:"Courier
New";color:black;mso-ansi-language:EN-US" lang="EN-US">; </span><span
style="font-size:10.0pt;font-family:"Courier
New";color:forestgreen;
mso-ansi-language:EN-US" lang="EN-US">% use non-linear
normalization</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>cfg.mri<span
style="mso-spacerun:yes"> </span><span
style="mso-spacerun:yes"> </span>= mri; </span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black;mso-ansi-language:
EN-US" lang="EN-US"><span style="mso-spacerun:yes"> </span>grid<span
style="mso-spacerun:yes"> </span>=
ft_prepare_sourcemodel(cfg);</span><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:
EN-US" lang="EN-US"><o:p></o:p></span></p>
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style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p> </o:p></span></p>
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style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;font-family:"Courier
New";mso-ansi-language:EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";color:black;
mso-ansi-language:EN-US" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoListParagraphCxSpFirst"
style="margin-bottom:0cm;margin-bottom:.0001pt;
mso-add-space:auto;text-indent:-18.0pt;line-height:normal;mso-list:l0
level1 lfo1;
mso-layout-grid-align:none;text-autospace:none"><!--[if !supportLists]--><span
style="font-size:12.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
minor-latin;color:black;mso-ansi-language:EN-US" lang="EN-US"><span
style="mso-list:Ignore">1.<span style="font:7.0pt "Times
New Roman""> </span></span></span><!--[endif]--><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";
color:black;mso-ansi-language:EN-US" lang="EN-US">It turns out
that my script works quite
well for most of my subjects, but in case of one single subject
I obtain a curious
grid which has no grid point in the region of the occipital
cortex/cerebellum (2<sup>nd</sup>
figure plotted in red). As you can see in the first figure the
subjects mri look
good and also do the template grid (2<sup>nd</sup> figure
plotted in green). I’m
wondering what went wrong. So what options do I have if the
warping/transform
algorithm goes wrong?<span style="mso-spacerun:yes"> </span><o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-bottom:0cm;margin-bottom:
.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:normal;mso-list:
l0
level1 lfo1;mso-layout-grid-align:none;text-autospace:none"><!--[if !supportLists]--><span
style="font-size:12.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
minor-latin;color:black;mso-ansi-language:EN-US" lang="EN-US"><span
style="mso-list:Ignore">2.<span style="font:7.0pt "Times
New Roman""> </span></span></span><!--[endif]--><span
style="font-size:12.0pt;mso-bidi-font-family:"Courier
New";
color:black;mso-ansi-language:EN-US" lang="EN-US">Why is the
template rotated and shifted when
comparing it to the subjects grid (2<sup>nd</sup> figure bottom
right)?</span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-bottom:0cm;margin-bottom:
.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:normal;mso-list:
l0
level1 lfo1;mso-layout-grid-align:none;text-autospace:none"><br>
Thank you in advance,<br>
Maria<br>
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