Hi Arun,
The output from flirt is always the same size as your reference volume.
If you want to get a smaller voxel size in your output image, then your
reference must have the size you want. It seems that currently your
reference has larger voxels than your input so is doing the opposite
of what you want. Note that the intensities in the reference image
are *ignored* - when using applyxfm it is only there to provide the
voxel size and FOV.
If you find this confusing, try using the ApplyXFM gui, which allows
you to specify the output size directly, as an alternative to using a
reference image.
All the best,
Mark
On Monday, September 8, 2003, at 01:40 pm, Arun Bokde wrote:
> Hi all,
>
> I am using flirt to interpolate a file to smaller size voxels and it is
> not quite working the way I want it to. The command I am using is
>
> flirt -in input.hdr -ref ref.hdr -applyxfm -init transfer.mat -interp
> nearestneighbour -out output.hdr
>
> where the input is a file with 181 x 217 x 181 voxels, each voxel 1 x 1
> x1 mm.
> The reference file is 91 x 109 x 91 voxels, with each voxel 2 x 2 x 2
> mm. The transfer.mat file is a file that contains the following matrix
>
> 1 0 0 0
> 0 1 0 0
> 0 0 1 0
> 0 0 0 1
>
> The output file that I get is one where each slice now contains 4 of
> the original slices. It seems like the FOV has changed (am I right?).
> What I am missing in the above command ?
>
> TIA.
>
> Best, Arun
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