Dear Jeung,
flirt -ref MNI152_T1_2mm_brain.nii -in Aanat2_bet.nii -omat exam_anat2mni.mat
fnirt --in=Aanat2.nii --aff=exam_anat2mni.mat --cout=exam_nonlinear_transf
--config=myconf_T1_2_MNI152_2mm.cnf
applywarp --ref=MNI152_T1_2mm.nii --in=Aanat2.nii
--warp=exam_nonlinear_transf --out=exam_warped_Aanat2.nii<fnirt2mm.png>
It is not obvious what has gone wrong. You must also forgive my ignorance about AFNI. What is it that I actually see in the AFNI display? Is the problem that only one quadrant of the data has been filled in, or is there a swap of axes as well?
If it is the fact that only one quadrant was filled in I would suspect that there is a difference between the file that you specified as --ref for fnirt and that which you specify for applywarp. I assume that the --ref is defined in myconf_T1_2_MNI152_2mm.cnf. Could you please check it and make sure that the --ref line in there says something like
--ref=MNI152_T1_2mm.nii
Please also remember that the parameters can override themselves. So if you e.g. have something like
--ref=MNI152_T1_2mm.nii
... Other stuff...
--ref=rubbestad.nii
the latter will take precedence.
If that isn't the problem maybe you can upload all the files to our website and email me (off the mailbase) the reference number that you are given.
Good luck Jesper
