[FieldTrip] Atlas used for 15684 vertices sourcemodel

Wed May 10 09:02:20 CEST 2023

Hi Fan,

If it is your intention to do a cortical surface based source reconstruction, where you have managed to create the individual surface aligned cortical sheets, it suggests that you have managed to successfully run the ft_postfreesurferscript.sh. If memory serves me well, the output to this script will also contain the topologically equivalent low-resolution versions of the freesurfer generated automatic parcellations (look for files with ‘aparc’ in the name). These can be read in with ft_read_atlas. If this eventually works for you, but does not give the desired results that allow you to answer your scientific question, then one could consider another parcellation.

Good luck,
Jan-Mathijs

On 8 May 2023, at 16:25, Puluto Go via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi Paolo and other experts,

If it is convenient, could you please give a sample script or a bit of detailed instruction on the procedure below,
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, which was specified here, https://mailman.science.ru.nl/pipermail/fieldtrip/2021-March/040784.html.

I appreciate it a lot in advance.

best,
Fan

On Mon, 8 May 2023 at 14:50, Puluto Go <gopuluto at gmail.com<mailto:gopuluto at gmail.com>> wrote:
Hi Paolo,

Thanks a lot for your quick reply. Could you please send me the link to download the Glasser Atlas?

best,
Fan

On Mon, 8 May 2023 at 14:25, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:
Hi Fan.

You can get the freesurfer generated mesh of the Glasser Atlas from the webpage of the van Essen et al. paper and decimate that consistently with the sourcemodel through the ft_postfreesurferscript.

Best,

Paolo

On Mon, May 8, 2023 at 2:04 PM Puluto Go via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Dear FT experts,

Hope you all are doing well. I used the standard pipeline, https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/sourcemodel/__;!!HJOPV4FYYWzcc1jazlU!4xhtw8gBTkdg03h0-bqXerFr7vc5oMP3t7NpXjxfpPemszKTZL8w5-CBk8fodYz-aqphk80lyZxFEK0FZU3G-K7v23n0nNYLRe0Vbg$ <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/sourcemodel/__;!!HJOPV4FYYWzcc1jazlU!_hjVO1VbUWG0broPdCxr7Xqn2ppQIvubNCHuUYo04PEDDWmABEcO5XV2tM_Gl1QGRDW3hBeXdouBSg2J8PsX0A$>, to generate a source mesh for each of my participants. The procedure resulted in a 15684 vertices mesh for each participant. My questions are as follows.

1), If there is an atlas corresponding to the 15684 vertices mesh in the workbench output. If so, could you please tell me how it is named?  May I use ft_read_atlas to read it?

2), the second one relates to the thread here, https://mailman.science.ru.nl/pipermail/fieldtrip/2021-March/040784.html, in which (the second solution) you specified the procedure to extract an atlas for source mesh with 15684 vertices, could you please elaborate it a little bit on how to do this? or are there template scripts in FT toolbox to do this?

Thanks a lot for your help in advance.

best,
Fan
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