Dear Hanna,
> I have two questions:
>
> First (FNIRT): Can I use the parameters of the T1_2_MNI152_2mm.cnf-
> file to
> register my T1-1mm-pictures to MNI..._1mm ?
You can, but it would take a very long time. It is better to edit it
so that the final --subsamp level is 2, i.e. multiply all --subsamp
values by 2.
Having said that, why do you want to register to the 1mm template. If
you are using a warp-resolution of 10mm fnirt cannot use that extra
information anyway. I would suggest you still register to the 2mm
template, and then when you run applywarp to obtain the final
resampled images you give the 1mm template as the --ref scan, which
will mean your images get resampled into that space.
> Second (TBSS): Does the ...to_target_warp.nii.gz-file include the
> resulting
> Matrix-file of flirt and the resulting warp of fnirt?
Yes.
Good luck Jesper
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