Dear Ed,
I'm afraid I don't really understand your problem.
You want just a translation, but the "orientation of both volumes are different" and so you are unhappy with just a translation. Do you mean that there is a fixed rotation (or rotation/scale/skew) that you also want to apply? Can this be determined from the scanner coordinates (via the qform/sform)? How do you know that they will match if you only apply a translation? Sorry, I just cannot quite figure out what you want/mean.
All the best,
Mark
On 22 Apr 2013, at 12:11, Ed Gronenschild <[log in to unmask]> wrote:
> Hi,
>
> 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 volume?
>
> Cheers,
> Ed
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