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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