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Hi Robert,
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<div class="">If you process the cortical sheet that is shipped with the Conte69 atlas, i.e. pass it through freesurfer_to_fs_LR, and then through mne_setup_source_space, you’ll get a topologically valid low-resolution parcellation, which you could use with
your individual source models. Each of the vertices is surface-registered by construction.</div>
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<div class="">Best,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 21 Jul 2016, at 17:19, Seymour, Robert (Research Student) <<a href="mailto:seymourr@aston.ac.uk" class="">seymourr@aston.ac.uk</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear Fieldtrip Forum,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I'd just like to pick up from an old thread posted to the FT forum: <a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009682.html" class="OWAAutoLink" id="LPlnk682423" style="font-size: 10pt;">https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009682.html</a>. <span style="font-size: 10pt;" class="">Basically,
I am trying to perform </span><span style="font-size: 10pt;" class="">source localisation using regions within</span><span style="font-size: 10pt;" class=""><span class="Apple-converted-space"> </span>an atlas described on the Conte69 brain </span><a href="http://brainvis.wustl.edu/wiki/index.php//Caret:Atlases/Conte69_Atlas" class="OWAAutoLink" id="LPlnk83615" style="font-size: 10pt;">http://brainvis.wustl.edu/wiki/index.php//Caret:Atlases/Conte69_Atlas</a>.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have run the standard Freesurfer pipeline on my MRIs (in head co-ordinate system), converted the output to the <span style="font-family: Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 13.3333px;" class="">Conte69
atlas using</span> <span class="">“freesurfer_to_fs_LR” pipeline, and finally down-sampled the mesh using the helpful instructions from the above thread, combined with MNE function: <span class="">mne_setup_source_space --ico -6 .</span></span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">So to my </span><span style="font-size: 10pt;" class="">questions: </span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">i) How do I map from the atlas vertices (on the 327684 vertex Conte69 brain) to the downsampled mesh with 4096 vertices per hemisphere? I feel it has something to do with the deformation maps...</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">ii) How to I align everything in the head co-ordinate system (appreciate this is a bit of a general question)?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Many thanks, </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Robert Seymour (PhD Student, Aston Brain Centre)</div>
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