Dear Radhika,
The commands you have used are exactly right.
The only reason there is a difference is that your FOV is (240mm x 240mm
x 186mm) while
the avg152 has a FOV of (182mm x 218mm x 182mm).
Therefore you are looking at a larger area of real space.
I would expect that you should get no cropping of the brain at all while
the image will be off-centre
because the extra bit of FOV will be made up of zeros (or appropriate
background values).
Everything in flirt (esp. the matrices) uses mm, and the "origin" is
just the bottom left corner of
the first slice (the first voxel written in the file). Therefore if you
have two different sized volumes
they will be aligned at this corner, and the bigger one will extend
further away from this corner.
The reason this is chosen, rather than the centre of the volume (COV),
is then the matrix doesn't need to
know anything about the volumes that created it - it is totally
independent, which is handy.
If you want the extra FOV to be distributed evenly at both edges,
effectively aligning the COV,
then you can do this with a second transformation matrix that you
concatenate to your first.
This second matrix in your case would be:
1 0 0 -29
0 1 0 -11
0 0 1 -2
0 0 0 1
The values in the right hand column are the translational offsets in mm,
calculated by:
(182-240)/2 = -29, (218-240)/2 = -11, (182-186)/2 = -2
Hope this explains everything.
If you still have worries about the cropping, I'd need to look at the
data (don't send it to the list though).
All the best,
Mark
Radhika wrote:
>Hi,
>
>I apologize for the repitition of this topic but even after browsing the
>previous postings on this topic I am not able to get the following to work.
>
>I have an image (file1) at a higher resolution (256x256x124) and smaller
>pixel size (0.9375x0.9375x1.5) than avg152T1.img. I would like to transform
>this image into the standard space while maintaining the resolution. I use
>the following two steps for this transormation...
>
>
>a) flirt -ref avg152T1.img -in file1 -omat matfile -out tmp
>b) flirt -ref file1 -in file1 -applyxfm -init matfile -out file1_std
>
>The pixel size and FOV of the output (file1_std) are same as the original
>image (file1) but the image, file1_std, appears cropped and off center in a
>square display window unlike the original image (file1). Is the
>transformation matrix relative to the image dimensions of avg152T1.img?
>
>I am not able to understand the origin of this and would appreciate any
>help.
>
>thanks in advance,
>radhika
>
>
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