HI - this wouldn't be trivial using the SIENA framework because it finds the movement of the brain/nonbrain boundary - and for a lot of the cerebellum it's boundary is touching other (cortical) brain regions.

I think to do the best job of longitudinal cerebellum volume change you would want to do something like: run FLIRT+FNIRT between the two timepoints, and within a cerebellum mask (eg derived from a standard space mask), integrate the jacobian of the warp field across the region.

Cheers.





On 2 Nov 2017, at 06:45, Sherry Chen <[log in to unmask]> wrote:

Hi FSL community,
 
Recently I have been trying to work out the possibility of doing volumetric analysis on the cerebellum using SIENA package.
 
To my knowledge, as SIENA is designed to analyse the motion of the brain edge between time points, a whole brain edge mask would be used for the cross-subject statistics in randomise. Actually my interest is about the cerebellum. I know how to create a mask of the whole cerebellum. I was wondering if there is a way to create a mask of the cerebellar boundary/edge that could be used in the SIENA voxelwise statistics?
 
Any suggestion is more than welcome :)
 
Thanks,
Sherry


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