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Dear Ben, I have a vague recollection of there once being a bug that caused images to look like that when outside the original FOV. Can you just confirm for me that you are using the latest version of FSL? Jesper On 22 Aug 2011, at 22:29, Benjamin Kay wrote: > I am trying to apply a linear transformation using the --premat option of applywarp. The reason I am trying to do this is so that I can apply a linear and a non-linear transformation simultaneously, thereby interpolating once rather than twice. Unexpectedly, the output of applywarp and ApplyXFM are substantially different. The output of ApplyXFM is what I expect to see. The output of applywarp has some kind of artifact along the superior margin of the brain. Does anyone know what this artifact is or what I am doing wrong? Is this a bug in FSL? > > Screenshots are attached to this e-mail. If you wish, you can download the NIFTI files needed to reproduce this issue from my personal website. > reference volume: http://benkay.net/fsl/anat-brain.nii.gz > input volume: http://benkay.net/fsl/mean-func.nii.gz > transformation matrix: http://benkay.net/fsl/mean-to-anat.mat > output of applywarp: http://benkay.net/fsl/applywarp.nii.gz > output of ApplyXFM: http://benkay.net/fsl/ApplyXFM.nii.gz > > The transformation matrix was generated via: > fsl4.1-flirt -ref anat-brain.nii.gz -in mean-func.nii.gz -out ApplyXFM.nii.gz -omat mean-to-anat.mat -dof 7 -interp sinc > > applywarp was invoked thusly: > fsl4.1-applywarp --ref=anat-brain.nii.gz --in=mean-func.nii.gz --out=applywarp.nii.gz --premat=mean-to-anat.mat --interp=sinc > > ApplyXFM is, of course, a GUI. Run it with sinc interpolation or just use the output of flirt (above), which ought to be pretty much the same thing. > > All fun was had using fsl-4.1.8 on Debian unstable, Linux 3.0.0-1-amd64. > <applywarp.jpeg><ApplyXFM.jpeg>