Dear Ai,
> I met some problems about FA registration, the following is my protocol.
>
> 1) My DTI image voxel size is 2*2*2mm.
> 2)First I got FA map using FDT in FSL.
> 3) Then registering FA map to standard FMRIB58_1mm using FLIRT in FSL and got .mat file.
> 4) Last using following command line in terminal to FNIRT.
>
> fnirt --in=dti_FA_flirt.nii.gz --aff=dti_FA_flirt.mat --config=/usr/local/fsl/etc/flirtsch/FA_2_FMRIB58_1mm.cnf --cout=coef_dti_FA_to_FMRIB58 --iout=dti_FA_fnirt --jout=jac_dti_FA_to_FMRIB58 --jacrange=0.01,100
>
> But the results is terrible(the following image), where did I go wrong?
I think your command looks fine. Often when fnirt fails spectacularly, as in your case, it is because it has been given a poor initial start by the --aff transform. I suggest you first check how good dti_FA_flirt.mat is. If that looks good you can upload your data to us (through our uploading service) and we'll have a look at them for you.
Jesper
> <屏幕快照 2012-11-21 下午2.19.50.png>
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