Hi Eric,
To get a more general DOF for 2D you need to use the custom schedule
files in the $FSLDIR/etc/flirtsch directory. The one you want is
sch2D_6dof
but note that there are others you can try too.
To use a schedule file just do something like:
flirt -2D -in sliceI -ref sliceR -out result -schedule
$FSLDIR/etc/flirtsch/sch2D_6dof
together with any other options you'd normally use.
There's also a brief tutorial on that at:
http://www.fmrib.ox.ac.uk/fslcourse/flirt_fugue/_7090.fpd/index.html
All the best,
Mark
Erik-Jan Vlieger wrote:
>Hi,
>
>We are currently trying to correct for Eddy currents induces by diffusion
>weighted imaging. The effects can be modeled using affine transformations,
>and therefore we would like to use Flirt. However, we would like to do slice
>by slice matching (2d), and allow for translation, rotation, magnfication and
>shear. So using flirt with the option "-2d" would not work.
>If I were to create an analyze file with just one slice in the z-direction,
>and match this to another one-slice-analyze-file, would this work? Would the
>in-plane translation, rotation, magnfication and shear be calculated
>correctly, and the through plane effects be left alone?
>
>Thanks a lot,
>Erik-Jan Vlieger
>
>
>
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