Hi Paul,

Thank you for your prompt help.

> Basically, my guess is that your dset starts out
> far from overlapping on the template dset; you
> can check this with:
>

> 3dcopy  ${T1_data} test_copy.nii
> 3drefit -space TLRC test_copy.nii
>

Yes, the T1 and the template did not overlap (see A in the attachment).

> In your particular case, I think this happens
> because of purging the obliquity information with
> "-deoblique_refitly"
> You could deoblique your anatomical with 3drefit,
> and then use a similar @Align_Centers command to
> what I used above. Note that removing the
> obliquity information might mean that your
> anatomical and EPI don't align well...

The overlap improved after running the commands you suggested (see B in the attachment). These are the commands I've run:
3drefit -deoblique T1_copy.nii
@Align_Centers -cm -prefix T1_new.nii -dset T1_copy.nii -base MNI152_2009_template_SSW.nii.gz


However the anat_SS is still not looking ok (see C in the attachment). This is the command I've run:
@SSwarper -input T1_new.nii -base MNI152_2009_template_SSW.nii.gz -subid sub02 -giant_move -odir .

> What is the output of:
>

> 3dWarp -disp_obl_xform_only -deoblique ${T1_data}
>

# mat44 Obliquity Transformation ::
0.996334 -0.061114 -0.059856 7.780968
0.035478 0.931914 -0.360941 -8.087494
0.077839 0.357494 0.930666 -69.402573

The skull-stripping for this participant looked pretty good when using @NoisySkullStrip (see D in the attachment). Would it be at all possible to feed a skull-stripped brain to @SSwarper?

Thank you!

All the best,
irene