Hi,
I am attempting to run BET on a DTI scan i've acquired sagittally but i want to include the entire brainstem. When running BET from the GUI and tweaking the -f and threshold gradients, i am unable to get what i need. So, i manually drew in the mask on the brainstem and then ran "fslmaths -add" to combine the two masks, and then "fslmaths -bin" to make sure i didnt get any overlapping voxels. Now that BedpostX is running, my next problem is figuring out how to apply this mask to the entire data.nii.gz file and create a nodif_brain.nii.gz using the mask i've created. Can this be done? I searched the forums for "manual BET" but to no avail.
Thanks in advance!
Joe
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