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
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