T2 doesn't align too well?

[soichih]

I've aligned t1 and t2 from CSI1 BOLD5000.

The t1 seems to align well, but not t2.

It's using t2 version of the template, so I am not sure what's going wrong.

+ flirt -interp spline -in input_robustfov.nii.gz -ref templates/MNI152_T2_1mm -omat roi2std.mat -out acpc_mni.nii.gz

[bacaron]

I'm so sorry to get to this so late @soichih. Is this still an issue? The image you provided looks fine to me.