Hi,
It would be better to use fslmaths with the -roi option for this as it maintains the image FOV. See the first practical in the FSL course if you are unsure how to use fslmaths.
All the best,
Mark
Eduardo Garza <[log in to unmask]> wrote:
Dear FSL users
Perhaps this is an easy question, I do hope so, but I haven't found an answer in the forum yet.
I created two binary masks for the Right and Left corticospinal tract (CST) respectably, using the JHU White-Matter Tractography Atlas. Now I wish to subdivide the mask into different regions of each CST such as a bulbar region, mesencephalic region and so forth. This way, I want to get 4 regions masked per CST to use as ROIs for mean FA extraction.
Is there a way to do this inputing the z-axis range instead of doing it by hand using the mask editor in FSLVIEW? Perhaps using fslroi?
Thank you in advance,
Best regards
Eduardo
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