AFNI proc fails to properly align the EPI to the anatomical dataset for one specific subject. The resulting EPI brain by AFNI proc is completly misaligned.
Here is how I proceeded.
First, deoblique was required because the dataset was very oblique.
3dcopy $directory_raw/anat1to3d+orig Temporary 3drefit -oblique_recenter Temporary+orig 3drefit -deoblique Temporary+orig 3dcopy Temporary+orig Anat1_deoblique rm Temporary+orig.BRIK rm Temporary+orig.HEAD
Testing the overlap via the following code resulted in very good EPI-Anat overlaps for all subjects, except for subject 5 that is causing problems here.
@djunct_overlap_check \ -ulay Anat1_deoblique+orig \ -olay Rest2_deoblique+orig \ -prefix img_olay_epi_anat
Second, I ran SSwarper without extra options. The SSwarper results for subject 5, which are of course forwarded to AFNI proc, are fine.
@SSwarper \ -input $directory_processed/Anat1_deoblique+orig \ -base MNI152_2009_template_SSW.nii.gz \ -subid $subject \ -odir $directory_sswarper_1
The image in the attachment of this post shows the EPI-anat overlap for subject 5 after the first deoblique code shown above. It is clear to see that the overlap is not good. However, adding -giant_move or even -ginormous_move in AFNI proc does not solve the problem for this specific subject. I tried out different cost functions beside lpc+ZZ too, such as lpa and nmi. This did also not help.
What further possibilities do I have to achieve a proper alignment for this subject?