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FSL  August 2011

FSL August 2011

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Subject:

Re: applywarp and ApplyXFM produce different output

From:

Benjamin Kay <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 22 Aug 2011 18:51:23 -0400

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On Monday, August 22, 2011 17:59:13 you wrote:
> 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>
>
> 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
> 

I am using the Debian build of fsl-4.1.8, which I am given to believe is the 
most recent stable release.

fsl4.1-applywarp
Part of FSL (build 416)
applywarp (Version 1.2)

fsl4.1-flirt -version
FLIRT version 5.5

I am not afraid to go playing in the source code, so if you happen to have a 
reference to the FOV bug handy then please do share.

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