Hi Mark,
Thanks for your quick reply.
The problem was indeed in the transformation matrices: the decimal separator in the last column got shifted two places.
Unfortunatelty I still don't get the result I was hoping for (I guess this has to do with the definition of my transformation matrices), but at least the images are in view again.
Regards,
Birgit
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: vrijdag 25 januari 2013 10:43
To: [log in to unmask]
Subject: Re: [FSL] Affine transformation matrix in ApplyXFM
Hi,
This is probably due to you setting the values within the matrix incorrectly, or it not being saved as plain text (although you seem to have been careful about that). The single value that gets put in the background is the estimate that FLIRT makes from the original image of what the background value is. So it is equivalent to your brain being moved completely outside of your FOV, probably because the matrix is incorrect.
All the best,
Mark
On 25 Jan 2013, at 09:00, Birgit P <[log in to unmask]> wrote:
> Hello,
>
>
> I have a problem running the Applyxfm GUI.
>
>
> I have manually created an affine transformation matrix called CT1toMR2.mat (to transform image CT1.nii to MR2.nii).
> I've created this as a txt-file in Notepad and then manually changed the extension to .mat in my VMware Player used to run FSL.
> When I run ApplyXFM with this matrix, it works fine.
>
> However, if I use 'gedit' to adapt some values in the matrix and save it to CT1toMR2_2.mat it doesn't work anymore.
> If I open the transformed image in fslview, it seems to be filled with only one value (-1002.9) for every voxel.
> Also other matrices created in the same manner as CT1toMR2.mat (but for different input images) give single value output images.
>
> What can be the problem here?
>
> I've tried saving and running the transformation matrices in several kinds of ways, but I can't seem to reproduce the result as created with CT1toMR2.mat.
>
>
> Regards,
> Birgit
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