Dear Ben,
This is the most recent release.
I think that what you are seeing is not a bug but simply an arbitrary masking
issue. In FLIRT (which is called by ApplyXFM) there is a -paddingsize option
to control this but in applywarp there is not. What to do in voxels where
the old image voxels overlap by around 50% is quite arbitrary and I think
you are just seeing the more inclusive choice. If you do not like this then I
suggest that you transform a mask by the same transform, threshold
it at a high value (e.g., 0.9) to exclude voxels with smaller partial
volume overlaps, and apply this to your output. That should mask
out the areas that you are concerned about.
All the best,
Mark
On 22 Aug 2011, at 23:51, Benjamin Kay wrote:
> 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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