[RESOLVED] Parcellation atlas for within-circuit analysis

Hi! I would like to know if there is a parcellation atlas to use in the command “parcellate_bold” for a within-circuit analysis for amygdala, brainstem, insula and anterior cingulate cortex.
Thank you,

Hi Giulia,

Welcome to the QuNex forum!

What exactly do you mean with the term “within-circuit analysis”? In other words, could you tell us a bit more about what you are trying to do. It will be easier for us to help you once we know exactly what you are trying to achieve.

Best, Jure

Hi Jure,
I’m trying to study the connectivity between amygdala, brainstem, insula and anterior cingulate cortex.
So, I would use a parcellation atlas in dlabel.nii format to use in the command parcellate_bold for obtaining the matrix connectivity between these four cerebral substructures.
Best, Giulia


Unfortunately, I (and my colleagues) do not know if such a parcellation already exists. You could create one yourself by merging relevant HCP (Human Connectome Project) regions. However, I am not sure if CIFTI data includes brainstem. Probably not?


In the folder MNINonLinear, I found the file aparc+aseg.mgz that has the areas of interesting. Is there a way to use this, maybe converting it in a dlabel.nii file? Do you know if this is possibile?
Thank you.

Hi there, this is a little outside of QuNex jurisdiction but we have created a parcellation at https://github.com/ColeLab/ColeAnticevicNetPartition that leverages the cortical parcels from Glasser et al. 2016 and includes subcortical parcels constrained by anatomical structures (including the brainstem and amygdala). It is already in CIFTI space and available as a dlabel.nii. Please free feel to check it out and let me know if it fits your bill.