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<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">Hello dear Fieldtrippers!</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">This is my first post on the mailing list, so I apologize if this looks a
bit confused. </span></p>

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<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">So I'm trying to use the WFU PickAtlas for Brodmann areas in what I think are
MNI coordinates to find specific regions inside of a brain (I'm coming from
electrical engineering background, so I can't do that "by hand") in
an individual whole-head MRI and I'm having issues getting sane results.<br>
<br>
I suspect that my workflow is the problem, so I would be very grateful if
someone could provide some advice as to what I should be actually doing. <br>
<br>
My original idea was to take MRI in CTF coordinates, convert it to MNI
coordinates and then just use atlas to make masks. From what I could gather,
it's not that simple. </span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">So here are examples of what I'm doing right now:<br>
<br>
ft_defaults;</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">%Let's read atlas</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">atlas =
ft_read_atlas('C:\REALY_LONG_PATH_TO_PICKATLAS\wfu_pickatlas\MNI_atlas_templates\TD_brodmann.nii');<br>
<br>
<br>
%Using Subject01from FT tutorials right now, for simplicity's sake.<br>
mri = ft_read_mri('Subject01\Subject01.mri');<br>
<br>
<br>
%Reslice, apply transformations<br>
cfg=[];<br>
cfg.dim=[256 256 256];<br>
mri_resliced=ft_volumereslice(cfg, mri);<br>
<br>
cfg=[];<br>
mri_norm1=ft_volumenormalise(cfg,mri_resliced);</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">%Unfortunately, this cuts off everything below the nose!</span></p>

<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">%Still let's take a look at the visualization with atlas<br>
<br>
cfg=[];<br>
cfg.inputcoord='mni';<br>
cfg.atlas=atlas;<br>
cfg.roi='brodmann area 4';<br>
<br>
mask4 = ft_volumelookup(cfg, mri_norm1);<br>
mri_norm1.mask4=mask4;<br>
<br>
cfg=[];<br>
cfg.atlas=atlas;<br>
cfg.funparameter = 'mask4';<br>
ft_sourceplot(cfg,mri_norm1)</span></p>

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<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">%The result doesn't look so good, big part of the area seems to fit inside
of the gaps between brain tissue!</span></p>

<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">So this doesn't seem to have worked out. My next attempt was to directly
use ft_convert_coordsys. This fixed the cutting issue, but it didn't solve the
problem of results looking strange.</span></p>

<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">So my other idea was to try with <br>
<br>
template=ft_read_mri('C:\PathToFT\external\spm8\templates\T1.nii');<br>
<br>
cfg=[];<br>
cfg.method='spm';<br>
cfg.coordsys='spm';<br>
mri_realigned=ft_volumerealign(cfg,mri_resliced,template);</span></p>

<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">But this produces very obviously wrong results, like coronal slices on
sagittal plane. </span></p>

<p class="MsoNormal" style="margin-bottom:12pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"" lang="EN-US">I'm also not sure if I should be trying to somehow transform an atlas to
fit the individual MRI that I'm using?<br>
<br>
All the best,<br>
Andreja Kostić<br style="mso-special-character:line-break">
<br style="mso-special-character:line-break">
</span></p>

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