Hi Mehul,
what versions are you using? FS 5.0 and the fixed mri_robust_register
from the wiki? If not, please get the most recent stuff first.
mri_robust_register uses intensities to register the images. Amazing
that it finds the registration for t1 to t2. I have never tried this and
am not sure why it worked in your case.
It is likely that mri_convert does not work in all situations if you do
not specifically pass the -rl flag. Usually it should take the target
geometry from the lta, but that might not work. So try to specify -rl
directly and see if it helps. If not let me know and I'll take a look.
Best, Martin
On Sat, 2010-10-23 at 02:43 -0700, Mehul Sampat wrote:
> Hi Folks,
> I am trying to troubleshoot an issue and I have not been able to find
> a solution yet.
> Here is what I am trying to do:
>
> 1. I used mri_robust_register to register a t1-weighted image to a
> t2-image.
> mri_robust_register works very well and i also got an lta file
> (t1-to-t2.lta)
>
> 2. now i also have the wm-mask from the freesurfer output. this was
> created using:
> mri_binarize --i aparc+aseg.mgz --wm --o t1-wm-mask-fs.mgz
>
> 3. Then I take the wm-mask to native space using:
> mri_convert -rl orig/001.mgz t1-wm-mask-fs.mgz t1-wm-mask-ns.nii
>
> 4. Finally, I want to apply the t1 white matter mask to the t2 image
> using the lta file generated in step 1. for this I use:
> mri_convert --apply_transform t1-to-t2.lta t1-wm-mask-ns.nii
> t1-to-t2.nii
>
> step 1-3 work fine. but when i try to apply the transform in the last
> step, the output is zeros.
>
> The output of mri_robust_register in step 1 is fine. Does
> mri_robust_register use mri_convert to apply the transform and
> create the output image ? Or am I making some error ?
> thanks
> Mehul
>
>
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