Hi,
I've had a look at your images and the diffusion ones have significant
distortion which
is probably making simple registration difficult. However, your
original images have
different voxel sizes and FOVs and using the identity transform with
the FSL conventions
does not align them - as you know. I tried aligning them with a
translation-only registration
and by aligning the centre of volumes (in 2D only, as in 3D it was
clearly wrong). The two
matrices that I used for these I include below. Try them and see if
either of them aligns
the images as they were originally with the other software you used.
I cannot tell myself
as I'm not familiar enough with the monkey anatomy and the distortions
mean that not
all parts of the image can align at any one time anyway.
You can generate the aligned images by saving the matrices as text
files (don't use
Word for this - use a simple text editor) and then applying:
flirt -in dodif_brain -ref burt_2_20071221_135718_4_mri-n3_brain -
init transform.mat -applyxfm -out nodif2struct
this will use the matrix stored in the file called "transform.mat" (it
can be called anything
you want) and output an image called nodif2struct (again, this can be
any name you like).
So try these and see if they do what you want.
All the best,
Mark
For centre of volume alignment:
1 0 0 -4
0 1 0 -4
0 0 1 0
0 0 0 1
Translation-only flirt result:
1 0 0 -4.18904
0 1 0 -2.02476
0 0 1 -0.856084
0 0 0 1
On 19 Mar 2008, at 15:20, Roman Loonis wrote:
> I have uploaded my b0 image, a bet-extracted b0 brain, my
> structural, and my brain-extracted brain. I uploaded the original
> structural and b0 images because they are originally perfectly
> registered.
>
> Roman
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