I want to translate a 3D volume to a ref. volume by using flirt, where
the orientations of both volumes are different.
It is impossible to get a translation only with flirt by specifying -
dof 3. It will
use -dof 6, resulting also in a rotation, although being small.
A possible solution is to use a predefined schedule file.
Using the command
flirt .... -schedule $FSLDIR/etc/flirtsch/sch3Dtrans_3dof -dof 6
indeed produces a translation only, however, the result doesn't match
the orientation of the ref volume.
How can I force the result to be in the same orientation as the ref