[FieldTrip] Issues creating the Glasser atlas for the 8k point mesh

Schoffelen, J.M. (Jan Mathijs) janmathijs.schoffelen at donders.ru.nl
Tue Jun 14 09:50:42 CEST 2022


Hi Paolo,

It’s been a while that those files were generated, so I don’t have a c(l)ue.

My guess would be that the biggest chance for success is to first resample the individual hemispheres (i.e. the meshes + the atlas specifications) to the specified lower resolution (using some variant of the ft_postfreesurferscript.sh) and only then try to merge the 2 hemispheres into a single data structure.

Best wishes,

Jan-Mathijs


On 13 Jun 2022, at 15:22, Paolo Belardinelli via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear Fieldtrippers,

I was trying to create the Glasser atlas for the 8K mesh exactly in the same way as it was done here for the 4K:

https://download.fieldtriptoolbox.org/tutorial/networkanalysis/<https://urldefense.com/v3/__https://download.fieldtriptoolbox.org/tutorial/networkanalysis/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dSISokckA$>

I found out that the annotation files given with the Glasser paper contain two unuseful and not declared parcels in the corpus callosum (one each hemisphere named "???").

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/<https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dQfIeFskQ$>

I eliminated those and tried to convert the annotation files into .gii with R. Unfortunately, when using ft_readheadshape for merging the two different hemispheres into one cortical sheet, I receive an error message that some field is missing from the gifti file.  (My plan was to then decimate the label file with the same approach of ft_postfreesurfer script)

Can somebody give me a cue on how the file linked above was generated?

Best wishes,

Paolo

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