Dear FSL Masters,
I am trying to work on a series of fetal images.
Obviously it is not possible to use bet, so I did it manually.
My main problem is the orientation of the image. The fetal brain is in a very variable position.
I did the following:
1. fslorient -deleteorient file
2. fslswapdim file 1 x y z file2 (changing x y z accordingly and without affecting radiological convention)
3. fslorient -setqformcode 1 file2
This seems fine for main orientation along axes, but the brain would need some further reorienting by rotation (pitch, roll and yaw). Which is the way to do it using FSL?
Do I need to set the origin? And how?
any help is wellcome
thank you
Angela
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