Dear Anna,
> I am trying to warp the MNI152 T1 2mm template to the FMRI58_FA_1mm template. I used the following commands for FLIRT and FNIRT:
>
> flirt -in MNI152_T1_2mm_brain.nii.gz -ref FMRIB58_FA_1mm.nii.gz -omat T1_FA_linear_transf -out T1_FA_linear_transf
> fnirt –ref=FMRIB58_FA_1mm.nii.gz –in=MNI152_T1_2mm_brain.nii.gz --aff=T1_FA_linear_transf.mat –cout=T1_FA_nonlinear_transf –iout=T1_FA_nonlinear_transf_image
>
> However, when I run fnirt, I get the following warning message:
> Requested tolerance not obtained. Requested tolerance was .001, and achieved tolerance was 0.18294. This may or may not be a problem in your application, but you should look into it.
>
> Then, when I try to apply my warps to a set of ROIs, fsl is unable to read my warping matrices.
I am not really sure what you are trying to achieve here. The two templates should be in approximately the same space already so you should not need to warp one to the other. You can overcome the difference in image matrix by running e.g. applywarp with a unity affine matrix and no non-linear warps.
It is also the case that fnirt (the nonlinear registration) cannot deal with vastly different contrasts (such as FA vs T1), but has been designed for warping images with similar contrast to each other.
Finally, for future reference, it is not recommended that you run fnirt without a configuration file.
Good luck Jesper
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