Dear Paul,

It seems that using @Align_Centers with no deobliquing either at 3drefit or @SSwarper resulted in good skullstripping and alignment.
Attached are screenshots from the index.html files using the first setting vs the current one.

The first setting used (see A in attachments) :
@SSwarper -input ${T1_data} -base MNI152_2009_template_SSW.nii.gz -deoblique_refitly -subid ${sub_id} -giant_move odir .

I got very similar results when using the following scripts (see previous post for details) :
3drefit -deoblique T1_copy.nii
@Align_Centers -cm -prefix T1_new.nii -dset T1_copy.nii -base MNI152_2009_template_SSW.nii.gz
@SSwarper -input T1_new.nii -base MNI152_2009_template_SSW.nii.gz -subid ${sub_id} -giant_move -odir .

The new setting uses: (see B in the attachments):
@Align_Centers -cm -prefix T1_new.nii -dset T1_copy.nii -base MNI152_2009_template_SSW.nii.gz
@SSwarper -input T1_new.nii -base MNI152_2009_template_SSW.nii.gz -subid ${sub_id} -giant_move -odir .

It looks like for both sub05 (which had very poor skullstripping using the first script) and sub09 (which had good skullstripping using the first script) the skullstripping and alignment is improved, when using the new setting.

The data we’re using is oblique. Could you help me in understanding why the results are better when not using deoblique?

Thank you.

All the best,
Irene