Hi FSL users,

I have been trying to figure out how to extract the WM volume for just the uncinate fasciculus (UF) in FSL and have had no success.

I know how to :

• register the T1 weighted image to MNI space
• perform segmentation of the T1 weighted image into GM WM and CSF
• extract the whole brain volume of these 3 tissue types

I thought I could create a mask of the UF in MNI space (JHU WM atlas) and apply the above steps to extract the WM volume of just the UF mask area but keep hitting road blocks.

Any suggestions would be greatly appreciated :)