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...), 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.