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Dear Paolo,
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<div class="">@1: I have not encountered the issue you describe. Probably it is the consequence of the fact that the anatomical images you use are different as compared to ours, e.g. in terms of voxel sizes, field-of-view, acquisition sequence. I am no expert
in mri_convert, but this function has some options that might tweak its behavior such that it does justice to your anatomical images.<br class="">
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<div>@2: If you run the post processing script (which relies on hcp-workbench) the meshes will be surface-registered to a template, which allows for direct vertex-wise comparison across subjects (as well as across hemispheres).</div>
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<div>Best,</div>
<div>Jan-Mathijs</div>
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<div class="">On 2 Oct 2019, at 11:35, Paolo Belardinelli <<a href="mailto:paolo.belardinelli@gmail.com" class="">paolo.belardinelli@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Dear all,
<div class="">I would first like to thank Jan-Mathijs for the massive work on the mesh sourcemodel.</div>
<div class="">I encountered a couple of minor issues while implementing the whole process:</div>
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<div class="">1. In some subjects, after saving the .mgz file with Fieldtrip (including acpc coordinates and reference point), the image is slightly shifted towards the superior side of the frame by mriconvert (<span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">mri_convert</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-o" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(102,102,102)">-</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">c</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-o" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(102,102,102)">-</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">oc</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-mi" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(64,160,112)">0</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-mi" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(64,160,112)">0</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-mi" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(64,160,112)">0</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="err" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;border:1px solid rgb(255,0,0)">$</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">SUBJECTNAME</span><span class="gmail-o" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">mgz</span><span style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240)" class="">
</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">orig</span><span class="gmail-o" style="font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box;color:rgb(102,102,102)">.</span><span class="gmail-n" style="color:inherit;font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:inherit;background-color:rgb(240,240,240);box-sizing:border-box">mgz</span>).
This implies that the upper part of the brain is being chopped and the further segmentation process with recon -all makes no sense anymore. Has anyone the same issue?</div>
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<div class="">2. As far as I understand, an average, atlas-mapped mesh where to visualize pooled results is not generated. What would be a straightforward way of visualizing group results in standard coordinates? </div>
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<div class="">Best wishes,</div>
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<div class="">Paolo</div>
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-- <br class="">
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<div class="">--<br class="">
Paolo Belardinelli, PhD<br class="">
Neurology Department<br class="">
University Hospital Tuebingen<br class="">
Eberhard Karls University Tuebingen<br class="">
Hoppe-Seyler Str. 3<br class="">
D-72076 Tuebingen<br class="">
Tel: <a value="+4970712985894" class="">+49 7071 / 29 80478</a><br class="">
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https://doi.org/10.1371/journal.pcbi.1002202<br class="">
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