Hi,
This most likely depends on whether your images are radiologically or neurologically stored.
Can you send us the output of fslhd on the INPUT, REF and OUT images?
All the best,
Mark
On 9 May 2013, at 12:39, "Wood, Tobias" <[log in to unmask]> wrote:
> Dear list,
>
> I discovered the following while trying to resample some scans of the same subject, but with slightly different FoVs, to a cropped sub-volume of one of those scans. The following steps should reproduce the problem with any image, e.g. if INPUT.nii is 128x128x128, with FSL 5.0.0
>
> fslroi INPUT REF_0 0 64 0 64 0 64
> fslroi INPUT REF_64 64 64 64 64 64 64
> flirt -in INPUT -ref REF_0 -out OUT_0 -init $FSLDIR/etc/flirtsch/ident.mat -applyxfm
> flirt -in INPUT -ref REF_64 -out OUT_64 -init $FSLDIR/etc/flirstsch/iden.mat -applyxfm
>
> I would expect OUT_0 and OUT_64 to be perfect copies of REF_0 and REF_64 respectively. However, on my system, OUT_64 is a perfect copy of REF_0. This leads me to believe that the offsets contained within the qform/sform are not being respected properly, even though they all appear to set correctly in the various headers.
>
> If I run flirt with the -v option, I get the following warning:
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
>
> Is there anyway I can get OUT_64 to match REF_64? Is this a bug?
>
> Thanks in advance.
>
> Dr Tobias Wood
> King's College London, Department of Neuroimaging
> [log in to unmask]
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