hi,
then you effectively register a T1w image in individual subject space to a T2(*)w image in standard space. Note that FNIRT is not designed to handle this even if it may run ok in some instance. It would be better if you resample a T1w template to the dimensions of SPMs EPI template (see previous posts on this).
Cheers,
Andreas
Am 02.04.2014 um 14:57 schrieb Jie Yu <[log in to unmask]>:
> Dear all
>
> I am trying to convert fsl FEAT 1st level pre-processed images to SPM standard space.
> (to avoid doing the preprocessing again)
>
> I used FNIRT example in the fsl website:
> Registering functional data (or any non-T1 image data) to MNI152 (via structural scan)
> ---------------------------------------------------------------------------------------------------------------------------------------
> bet my_structural my_betted_structural
> flirt -ref my_betted_structural -in my_functional -dof 6 -omat func2struct.mat
> flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat
> fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
> applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_functional --warp=my_nonlinear_transf --premat=func2struct.mat --out=my_warped_functional
> ----------------------------------------------------------------------------------------------------------------------------------------
>
> So I simply replaced the MNI152_T1_2mm with EPI.nii in SPM (that image is in SPM standard space).
> Apart from this, I changed nothing.
>
> I then saw this warning message in the command line:
> ------------------------------------------------------------------------------------------
> Warning, Jacobian not within prescribed range.
> Prescription is 0.01 -- 100 and obtained range is 0.00750596 -- 2.19173.
> ------------------------------------------------------------------------------------------
>
> FNIRT did complete its job….and I could see the warped image, and it seems ok.
>
> But is it okay???
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