[FieldTrip] Combining left/right hemisphere atlases from Freesurfer output

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

Hi Michael,

You’d need to adjust the vertex indices as specified in the hemisphere specific triangulations (in fieldtrip this is the ’tri’ field, in generic matlab these are the so-called ‘faces’ of a mesh).

if you do cat(1, atlas.tri, atlas_right.tri), the numbers in the second part of this resulting matrix (running from 1:N2, where N2 is the number of rows in atlas_right.pos), should point to the (N1+1):(N1+N2) rows in atlas.pos (where N1 is the number of rows in atlas_left.pos). Currently, the numbers range from 1:N2, which points to a bunch of left-hemispheric points.

Solution: atlas.tri = cat(1,atlas.tri, atlas_right.tri+size(atlas_left.pos,1));

Good luck and best wishes,
Jan-Mathijs

PS: I would recommend to update your fieldtrip version to a more recent one. At some point addressing questions inspired by behavior of 5-year old code might not be worth our while.



On 26 Feb 2024, at 21:17, Michael Houston via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello,

I ran the ft_readatlas function on a surface based atlas as follows for later parcellation:

atlas_left = ft_read_atlas({'lh.aparc.DKTatlas.annot','lh.white'}, 'format', 'freesurfer_aparc');
atlas_right = ft_read_atlas({'rh.aparc.DKTatlas.annot','rh.white'}, 'format', 'freesurfer_aparc');
atlas_right.aparc = atlas_right.aparc + 36;

atlas = atlas_left;
atlas.pos = cat(1,atlas.pos,atlas_right.pos);
atlas.tri = cat(1,atlas.tri,atlas_right.tri);
atlas.aparc = cat(1,atlas.aparc,atlas_right.aparc);
atlas.aparclabel = cat(1,atlas.aparclabel,atlas_right.aparclabel);
atlas.rgba = cat(1,atlas.rgba,atlas_right.rgba);
save('dkt_test','atlas')

I combined both outputs together to visualize both parcellated hemispheres in the same plot, but what I end up with is a messy superimposition of both hemispheres within each other. What is the more appropriate way to go about merging both left/right atlases together into one? I could not find a Fieldtrip function that does so (I am running the 2019 version).

Thanks,
Michael
--
mjhouston2 at uh.edu<mailto:mjhouston2 at uh.edu>
MSBE '20, University of Houston
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https://doi.org/10.1371/journal.pcbi.1002202

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