Hi,
On 21 Nov 2012, at 06:20, Ai Qing wrote:
> Dear FSL experts,
>
> 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
What did you provide as --ref? It's not in your argument list above and the usage message of fnirt says it requires a reference image so is this just a typo?
>
> But the results is terrible(the following image), where did I go wrong?
> <屏幕快照 2012-11-21 下午2.19.50.png>
Cheers, Dave
--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
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URL: http://www.fmrib.ox.ac.uk/~flitney
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