Mismatch between parcellation nii and labels?

[bwinsto2]

Hello - thank you for making this great tool. I am attempting to use the Schaefer 400 S3 2mm combined atlas, but there seems to be a mismatch between the parcellation and the labels. Take, for example, SomMotB_Aud_2, which is in the Schaefer2018_400Parcels_17Networks_order_Tian_Subcortex_S3_label.txt file as Parcel #95. However, when I go to this parcel in FSLeyes, the SomMotB_Aud_2 parcel is actually under #83 (cross-referencing it with the regular Schaefer 400 parcellation).

I noticed that the only .nii parcellation file is in 7Network: Schaefer2018_400Parcels_7Networks_order_Tian_Subcortex_S3_MNI152NLin6Asym_2mm.nii.gz. Does this have anything to do with the problem? Am I misunderstanding something?

Thank you for any help.

[yetianmed]

Hi there, the nii image you look at in fsleyes is the 7 network nii but the lable file you indicate is 17 network. That's why it's different. You will find the consistency if you open the 7 network lable.txt file.

The nii parcellation is the same for 7 or 17 networks. The only difference is the label file. That's why I did not upload simply to save space.

Hope this addresses your questions.

[bwinsto2]

Hi Dr. Tian, thanks for your response. I understand that the 7 network label file corresponds with the 7 network nii. However, as you mentioned, the 17 network label file is different than the 7 network label file. not just in naming but also in order:

If the nifti parcellation is the same for 7 and 17 networks, then the 17 network label file should work with the 7 network nii, but that is not the case as my first post demonstrated.

Please let me know if I am missing something. I would like to use the 17 network label file, but as you can see, it does not work with the 7 network nii.

thanks, Brian