HI AFNI expert,
I have trouble aligning two anatomical scans acquired from 2 different scanners (for the same subject).
One is processed with 3dWarp -deoblique to generate the anat_overlay
The other one mprage was coregistered to a standard T1 image in SPM and saved in NIFTI format, so I'm hoping to coregister these two scans together along with the SPM activation map that was already coregistered with this mprage.
Here is what I did and for some reason the anatomical scans are just clearly not aligned (of course then the activation map is not aligned either). Any suggetion will be really appreciated!
3dcopy $anat_spm anat_fmri_afni+orig
3dcopy $activation_spm activation_afni+orig
3dWarp -deoblique -prefix anat_fmri_do anat_fmri_afni+orig
3dWarp -deoblique -prefix activation_afni_do activation_afni+orig
3dUnifize -input anat_fmri_do+orig -prefix anat_fmri_do_uni
3dSkullStrip -prefix anat_fmri_ns -input anat_fmri_do_uni+orig
3dSkullStrip -prefix anat_overlay_ns -input $anat_overlay
align_epi_anat.py -dset2to1 -dset2 anat_fmri_ns+orig. -dset1 anat_overlay_ns+orig. -child_dset2 activation_afni_do+orig. -big_move -anat_has_skull no -dset2_strip None -verb 1 -volreg off -tshift off -deoblique off
