afni.nimh.nih.gov

Hi Paul-

I think much of the problem is caused by how you Z-padded the image. It looks like you were taking out slices instead of adding. My final commands to get pretty decent alignment are below. I did skull strip both anatomicals.

#strip anatomical
3dSkullStrip -input anat.nii -prefix anat_ns.nii
#z-pad low-res image
3dZeropad -I 20 -P 20 -A 20 -S 20 -L 20 -R 20 -prefix T1_ZP.nii t1_dyn_contrast_acq4.nii
#now skull strip that low-res image
3dSkullStrip -prefix T1_ZP_ss.nii -input T1_ZP.nii
#move low-res image center back
3drefit -dzorigin 20 T1_ZP_ss.nii

#perform alignment with MutualInfo because of low contrast in image
3dAllineate -base anat_ns.nii -input T1_ZP_ss.nii -master anat_ns.nii -prefix spgr_al.nii \
-1Dmatrix_save spgr_to_t1_dyn.1D -cost mi -final wsinc5 -source_automask \
-autoweight -twopass -warp shift_rotate -verb -overwrite

Edited 3 time(s). Last edit at 07/18/2019 04:02PM by Peter Molfese.