Hi Steve,

"Alternatively, you could work out how to reduce the field-of-view to just include the brain of each time point before feeding the output of that into SIENA. You would use FSLView on each image to work out the field-of-view and then use fslroi to reduce the FOV of the image."

I created a whole brain mask for the animal brain using FSLView.

But, it is not easy to understand how to use fslroi.

fslroi <input> <ouput> <xmin> <xsize> <ymin> ...

I just don't know how to determine these parameters and when I am supposed to use the mask file in fslroi.

Would you kindly let me know how to reduce the field-of-view to include the brain?


Thank you,

Buyean

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