[FieldTrip] Conte69 Atlas-Based Source Localisation

[Schoffelen, J.M. (Jan Mathijs)]

Hi Robert,

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.

Best,
Jan-Mathijs


On 21 Jul 2016, at 17:33, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:

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.

Best,
Jan-Mathijs

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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