Hi again Antony,
>
> If I wish to use MNI152lin_T1_1mm image as the reference file, then I will
> need to create a T1_2_MNIlin152_1mm.cnf file?
> In this file,
> --ref=MNI152lin_T1_1mm
> What will be the -refmask?
Just a piece of advice here. Why do you want to use the 1mm template
instead? If you are estimating the warps with a resolution of ~8-10mm
(i.e. --warpres=10,10,10) the 1mm template is overkill and it will take
much longer to run without improving your results.
If the reason is that you want to do your final resampling to 1mm (i.e.
have your finished images at 1mm resolution) you can do that anyway. Just
do
fnirt --ref=MNI152_T1_2mm --in=my_ima --cout=my_warps --config=MNI...
applywarp --ref=MNI152_T1_1mm --in=my_ima --warp=my_warps
--out=my_warped_ima_at_1mm
Good luck Jesper
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