Hi,
All coordinates and vectors are in FIRST are in units of mm.
If you take the transformation matrix from the structural to
MNI space and run "avscale" on this you will get a matrix
(at the start of the output) called the "Rotation & Translation Matrix".
If you copy this matrix into a file and then run flirt with the
-applyxfm and -init option (you need to pass the filename of
the file with the matrix as the argument to -init) then you
can resample the structural image into the MNI space (use the
MNI as the reference image) with appropriate rotation
but not scaling or shearing.
Note that if your original FOV is very different from the MNI
then this might cause some problems in which case you may
need to create your own reference volume of a greater size
(but same voxel size in mm) using fslcreatehd.
I hope this is what you wanted.
All the best,
Mark
On 23 Sep 2009, at 12:47, Tom Hartley wrote:
> Dear FSL Experts,
>
> What are the units of the vectors in the FIRST vtk output files (shape
> analysis)?
>
> Relatedly, for structural analyses, it would sometimes be useful to
> convert
> coordinates from meshes and volumes into a space which preserves the
> shape
> and scale of the structures in real world units (mm) and obeys the
> sense
> (L-R, POST-ANT, INF-SUP), and origin of the MNI space but without any
> shearing, scaling etc. Is there a straightforward way to do this
> using fsl
> tools and information in headers and mat files?
>
> Best wishes,
>
> Tom Hartley
>
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