Hi all,
I have aligned a 2D frame ('image1') to a reference frame ('refimage') using flirt. I now wish to apply the same transformation to a third image ('image2'). The alignment of 'image1' was successful, and yet the result of using applyxfm on 'image2' results in a black image.
The command I used for the first alignment:
/usr/local/fsl/bin/flirt -in /mnt/hgfs/image1.nii -ref /mnt/hgfs/refimage.nii -out /mnt/hgfs/image1aligned.nii -omat /mnt/hgfs/image1transmat.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -2D -dof 12 -interp trilinear
The command I used to apply the transformation:
/usr/local/fsl/bin/flirt -in /mnt/hgfs/image2.nii -applyxfm -init /mnt/hgfs/image1transmat.mat -out /mnt/hgfs/image2aligned.nii -paddingsize 0.0 -interp trilinear -ref /mnt/hgfs/refimage.nii
Any ideas\solutions?
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