afni.nimh.nih.gov

Hi all,

I have a binary ROI in the original space that I had created using freesurfer. Now I'm using 3dallienate to transform it to tlrc space, but I don't get the tlrc ROI in the right location. Here's the line that I'm using:
3dAllineate -prefix stand_ROI -input ROI.nii -master anat_w_skull_warped+tlrc. -1Dmatrix_apply warp.anat.Xat.1D -final NN

I'm guessing that I'm not using the right matrix (warp.anat.Xat.1D). Is that the problem?

Thanks,
Ana