Thank you Daniel!

Just to make sure:

1. So it SHOULD work to remove the "-tlrc_opts_at -init_xform CENTER" option and to run @Align_Centers insead for the linear warping as well?

2. For the non-linear warping I should run @Align_Centers. Should I use the template as the base or the functional data?

@Align_Centers -base ~/abin/TT_N27+trlc. -dset T1+orig -cm
or
@Align_Centers -base fmri+orig. -dset T1+orig -cm

Beacuse neither of these methods work for neither for affine nor non-linear warping. I still get the cropping (for affine) and memory corruption (non-linear) problems. I think this is because I'm not solving the centerign issue. Even with the commands above I still get the "datasets are 70 mm apart" warning. So, what am I screwing up with the commands above? @Align_Centers does give me a set of base, dset and delta displace values (higher when using TT_N27 than the functional as base) so it seems that it finds the offset atleast.

The only way I can make this run (so far) is to only do the standard linear warping in combination with the "-tlrc_opts_at -init_xform CENTER" option.



Edited 1 time(s). Last edit at 04/12/2016 06:57AM by Robin.