Dear all,

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?

Thanks,
Philipp



Edited 1 time(s). Last edit at 04/10/2022 08:26AM by Philipp.