Problem in registration in a particular subject

AFNI Message Board
1

Dear AFNI team,

I am doing registration between EPI images and its T1. The registration is almost perfect in all subject except in one (73 of 74 subjects). I would like to attach the code that I am using to perform the registration.


align_epi_anat.py  -anat  T1 \
-epi  EPI \
-epi_base BASE_VOLUME  \
-epi2anat   \
-suffix _pre.nii  \
-anat_has_skull no \
 -epi_strip 3dAutomask  \
-volreg off -tshift off -deoblique off  \
-master_epi  T1 \
-cost lpc

I put tshift and volreg in ‘off’ because I already did those step in a preprocessing pipeline.
What could be a possible cause for a bad registration? I would also like to attach a jpeg of the subject who has the registration problem.

Thanks in advance,
Karel

registration.jpg

2

Some recommendations to try.

-cost lpc+ZZ
remove “-deoblique off”
Add “-giant_move” if both those are far off.

Doing motion correction separately introduces an extra interpolation. If you do all your processing with afni_proc.py, then only a single interpolation is performed, and there is less blurring of your data.

3

Thank you so much Daniel. It worked with -cost lpc+ZZ.

Best regards,
Karel