Hi Folks, <br>I am trying to troubleshoot an issue and I have not been able to find a solution yet. <br>Here is what I am trying to do:<br><br>1. I used mri_robust_register to register a t1-weighted image to a t2-image. <br>

mri_robust_register works very well and i also got an lta file (t1-to-t2.lta)<br><br>2. now i also have the wm-mask from the freesurfer output.  this was created using: <br>mri_binarize --i aparc+aseg.mgz --wm --o t1-wm-mask-fs.mgz<br>

<br>3. Then I take the wm-mask to native space using: <br>mri_convert -rl orig/001.mgz t1-wm-mask-fs.mgz t1-wm-mask-ns.nii<br><br>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:<br>

mri_convert --apply_transform t1-to-t2.lta t1-wm-mask-ns.nii t1-to-t2.nii <br><br>step 1-3 work fine. but when i try to apply the transform in the last step, the output is zeros.<br><br>The output of mri_robust_register in step 1 is fine. Does mri_robust_register use mri_convert to apply the transform and <br>

create the output image ? Or am I making some error ? <br>thanks<br>Mehul<br><br><br>