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

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

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

--
--
[Università di Trento]<https://urldefense.com/v3/__http://www.unitn.it/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dTLSsRNhw$>

Paolo Belardinelli, PhD

Center for Mind/Brain Sciences - CIMeC<https://urldefense.com/v3/__https://www.cimec.unitn.it/en__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dSMjbyeeA$>

University of Trento
Via delle Regole, 101, 38123 Mattarello-Trento (TN), Italy
Phone: (+39)0461-283097

[facebook]<https://urldefense.com/v3/__https://www.facebook.com/cimec.unitrento/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dQFP905RA$>[twitter]<https://urldefense.com/v3/__https://twitter.com/cimec_unitrento__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dS2dnd-ZA$>[instagram]<https://urldefense.com/v3/__https://www.instagram.com/cimec_unitrento/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dT3vWzLNA$>[linkedin]<https://urldefense.com/v3/__https://www.linkedin.com/company/cimecunitrento/about/__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dQTCPFJZA$>[youtube]<https://urldefense.com/v3/__https://www.youtube.com/channel/UCOCqJ8qkQnZN4jQFrBNkI6A__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dTRVRdN_g$>

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-UBLHHfFows9n9yQP2gcWoc3DRP9KeqhIzragDm0n-R5bKtWo8Vkw2kYT_dapvzOfkuyYh4GU1Lyumakh6JQWl7zuNZG7dSp-WxTdw$

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20220614/15481d89/attachment.htm>