Dear Petr,

> I've been impressed with FLIRT performance on cross-modality registration.
> Although I know that low-res -> hi-res registration is recommended,
> sometimes I like to register the hires volume or slices to the low-res T2*
> images. By default, my registered image (-out) is interpolated to the low
> resolution of the reference. Is it possible to keep the original high
> resolution for the output? How would I do that? AIR's reslice has this
> capability but I would have to fabricate the binary *.air transformation
> file out of the matrix saved by FLIRT.

I assume that you want to transform (e.g. rotate) your high-res to be
"aligned" with your low-res, but still keep the high resolution.
The difficulty is in deciding what Field of View (FOV) you want
because in general the low-res and high-res FOV are different.
I don't quite know why you want this and in general I wouldn't
recommend such a method, but here's how you can do it:

1 -
Flirt always works better when using the high-res as the reference.
Therefore I recommend always using the low-res as the -in and the
high-res as the -ref, and then inverting the matrix obtained if you
want to go from low-res to high-res.  This is done by:

flirt -in low-res -ref -high-res -omat low2high.mat -dof 6
convert_xfm -inverse -matonly -omat high2low.mat low2high.mat

2 -
The next step is to do the reslicing.  For this you need a volume (the
-ref) of the desired output size (number of voxels and voxel
dimensions).
So, if you want the output with the same resolution *and* FOV as the
high-res volume, then you can use the high-res as the reference in:

flirt -applyxfm -in high-res -ref high-res -out transformed-high-res
-init high2low.mat

This will now produce a transformed (e.g. rotated) version of the
high-res volume, as dictated by the high2low transform (which is
always in mm), but keeping both the high-res voxel dimensions and
the FOV.  If the low-res FOV is substantially different, then you
might find that this output volume is truncated.  In this case you
need to create a new -ref volume for the -applyxfm step which has
the desired voxel dimensions (like the high-res) but the same FOV
(in mm) as the low-res.

Hope this is what you want,
        Mark