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Hi - 
The FMRIB58 template is in already in MNI space. The FA_2_FMRIB58_1mm config file is designed for registering an FA image to the FMRIB58_FA template whereas the T1_2_MNI152_2mm config is for registering a T1 to the MNI T1 template. Trying to mix and match here is going to lead to suboptimal results. Regardless, the steps that you outlined should be fine to get your FA map registered to the FMRIB_FA image (indeed, these are the recommended steps from the FNIRT Wiki page).

On Thu, Jan 12, 2017 at 9:58 PM, John anderson <[log in to unmask]> wrote:
Dear FSL experts,
I used to follow these steps to register FA maps to FAMRIB58:

flirt -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm_brain -in my_FA -omat my_affine_transf.mat
fnirt --in=my_FA --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=FA_2_FMRIB58_1mm
applywarp --ref=${FSLDIR}/data/standard/FMRIB58_FA_1mm_brain --in=my_FA --warp=my_nonlinear_transf --out=my_warped_FA

Are these steps still correct to register FA maps to MNI152 by replacing FAMRIB58 by MNI152 and the relevant config file. Are there any technical issues that prevent such registration?

Thank you for any comment or suggestion

John



--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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