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ggseg / ggsegSchaefer

https://ggseg.github.io/ggsegSchaefer/
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200 parcel Schaefer atlas #3

Closed SimonaPWH closed 3 years ago

SimonaPWH commented 4 years ago

Dear Dr. Mowinckel,

I LOVE your package and would really like to make use of it more often. However, almost all atlas-based projects in my lab use the 200 parcel not the 400 parcel Schaefer atlas - are there any plans to include the 200 parcel one in the ggsegExtra repo?

-Simona

SimonaPWH commented 4 years ago

I have tried adding the atlas with the help of the excellent documentation online. However, when creating the atlas from the .annot using the make_aparc_2_3datlas command, i run into this error:

An error occured when creating atlas.Error in dt[[idx]] : recursive indexing failed at level 2

Any help would be really great! Thank you!

-Simona

drmowinckels commented 4 years ago

oh interesting! Can you provide for me the full command you used to try? and is it the annot that comes with freesurfer, or one you have made your self?

This would help me also try and see if I get the same, and then hopefully fix whatever is bugging.

SimonaPWH commented 4 years ago

Thanks for the quick response! I used the annot file that comes with the Schaefer atlas in the FSL subfolder (there is one for each parcellation). Would it help if I would share it with you?

shmello11 commented 3 years ago

Just wanted to check if there has been any update with regard to the Schaefer 200 atlas? Really enjoy the package, thanks for your work on it!

drmowinckels commented 3 years ago

Hi. Thanks for a bump on this issue.

We have a PR ongoing with more parcellations for this atlas. Note that these are not 100% debugged yet, but seems to be mainly in order. You can read about the ongoing conversation about this PR in #2 .

To install and test this PR, you can install directly from the contributors repository to test it out.

remotes::install_github("monicathieu/ggsegSchaefer")
zhenglukai commented 3 years ago

Hi. Thanks for a bump on this issue.

We have a PR ongoing with more parcellations for this atlas. Note that these are not 100% debugged yet, but seems to be mainly in order. You can read about the ongoing conversation about this PR in #2 .

To install and test this PR, you can install directly from the contributors repository to test it out.

remotes::install_github("monicathieu/ggsegSchaefer")

Thank you! This is really helpful. It would be great if these additional atlas can be merged into the main build of ggsegSchaefer.

drmowinckels commented 3 years ago

Hi! The atlases are now merged into the main build, and I hope they work out for you :)