[FieldTrip] Atlas compatible with the 15684 point sourcemodel mesh

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Sun Mar 28 14:35:11 CEST 2021


Hi Paolo,

No it isn’t. The idea behind the cortical surface reconstruction scheme - as advertised among others in the tutorial you refer to - is that the meshes are created according to the recipe from a given template, with a specific number of vertices. The recipe results in meshes that are topologically equivalent to each other, in which a given vertex in mesh A can be directly compared with the same (ordinal) vertex in mesh B. The atlas you refer to, and which I assume you found on https://data.donders.ru.nl/collections/di/dccn/DSC_3011020.09_410?4 is based on a cortical sheet that contains 8196 vertices. It has been created using an older version of the recipe in the tutorial, back in the days that we used the MNE-software (the compiled C-based code, rather than MNE-python) for the ‘downsampling’ of the Freesurfer generated meshes, followed by a Caret-based script for the surface registration.

I don’t think that it makes much sense to try and interpolate the different topologies on each other. So, there are 2 potential solutions here.
1) you generate your surface meshes using the old recipe, resulting in 8196-vertex meshes for your subjects.
2) you generate a low-resolution version of the Conte69 atlas using HCP-workbench, using the same spherical template meshes (mapping the 164k per hemisphere to the 8k per hemisphere meshes), and apply a ’subparcellation’ scheme to chop up the large Brodmann areas in smaller chunks.

Best wishes,
Jan-Mathijs



On 27 Mar 2021, at 20:37, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:

Hi Fieldtrippers.

Is there a cortical atlas available to interpolate with the sourcemodel mesh described here?

https://www.fieldtriptoolbox.org/tutorial/sourcemodel/

I found the atlas_conte69_8196reg_LR_brodmann_subparc.mat atlas in the donders repository. Is this the most appropriate atlas to interpolate my sourcemesh with?

Best,

Paolo

--
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[Università di Trento]<http://www.unitn.it/>

Paolo Belardinelli, PhD

Center for Mind/Brain Sciences - CIMeC<https://www.cimec.unitn.it/en>

University of Trento
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