[FieldTrip] Conte69 Atlas-Based Source Localisation

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Jul 21 17:33:44 CEST 2016

Hi Robert,

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.


On 21 Jul 2016, at 17:19, Seymour, Robert (Research Student) <seymourr at aston.ac.uk<mailto:seymourr at aston.ac.uk>> wrote:

Dear Fieldtrip Forum,

I'd just like to pick up from an old thread posted to the FT forum: https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009682.html. Basically, I am trying to perform source localisation using regions within an atlas described on the Conte69 brain http://brainvis.wustl.edu/wiki/index.php//Caret:Atlases/Conte69_Atlas.

I have run the standard Freesurfer pipeline on my MRIs (in head co-ordinate system), converted the output to the Conte69 atlas using “freesurfer_to_fs_LR” pipeline, and finally down-sampled the mesh using the helpful instructions from the above thread, combined with MNE function: mne_setup_source_space --ico -6 .

So to my questions:

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...

ii) How to I align everything in the head co-ordinate system (appreciate this is a bit of a general question)?

Many thanks,

Robert Seymour (PhD Student, Aston Brain Centre)

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