Subcortical region missing in LR 32k surfaces

[renxili]

Hi Dr. Dickie:

I notice that in the LR 32k surfaces, the subcortical region are missing. Is there any ways we can add the subcrotical regions? (some of our ROIs are in thalamus and cerebellum)

Best, Renxi

[edickie]

So yes, surf.gii files should only have surface data. And some analyses (i.e. the calculation of cortical thickness or curvature) can only be done on the surface. So those files may only include surface data.

CIFTI files should include data from subcortical structures where appropriate (i.e. for fMRI/BOLD scans). In general CIFTI format is like a container that houses data from the left surface, the right surface and subcortical data in one file. What type of data are you looking for?

[renxili]

We are looking particularly for the resting-state functional connection from cerebellum and its surrounding white matter (delete nuclei) to the cortical regions. Does it mean that we cannot "personalized" ROIs by PINT in the subcortical regions? Also, as we are trying to put the personalized coordinates back into CONN (which is the analysis tool we use for functional connectivity), is there a way to translate the new vertex IDs in the PINT output to the standard MNI coordinates?

[edickie]

Sorry, PINT is a technique developed for the cortical data. You might want to look at other techniques for the cerebellum. I have (in a paper in prep) used the Buckner parcellation) to extract data from the cerebellum (in a non-individualized manner) which i then combined with the PINT outputs to look at cortico-cerebellar connectivity.

To do an individualized cerebellum approach you would need another technique.