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Hi Robert,
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<div class="">Here I am again. I forgot to add to my previous message that you need to look into the sourcemodel.orig.inuse field to find out which vertices in the high resolution cortical sheet are used in the downsampled version.</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 17:33, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>> wrote:</div>
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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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