Hi Freesurfer experts,

I have several nifti images (created with another software) in the subjects original anatomical space (native space) that I want to transform to a common space (freesurfer version of MNI305 should be fine) using non-linear transformation.

Reading a previous answer regarding this issue (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033556.html), I understand I should use the mri_vol2vol command to apply the transformation stored in the file mri/transforms/talairach.m3z (I already run recon all). But after checking the result, the images are still not align with each other and do not resemble the mni305.cor.mgz file.

I used the following command:

mri_vol2vol --m3z my_subjects_dir/sub_X/mri/transforms/talairach.m3z --noDefM3zPath --reg_header --mov file_loc/img.nii.gz --targ /usr/local/freesurfer/average/mni305.cor.mgz --o file_loc/img_warped.nii.gz

I also tried without the --reg_header option with no success.

Any idea what I am doing wrong? can you give me an example that works?

Thanks in advance!

Gidon l.