Dear Ed,
> Processing functional and anatomical data by means of some package resulted
> in the following aligned data (all in standard axial orientation):
> - anatomical: anat.nii.gz (176x240x256, 1x1x1 mm^3 voxel size)
> - functional: funct.nii.gz cropped to 35x49x27, 3.5x3.5x5.2 voxel size)
>
> I extracted the first volume from the functional data, called funct0.nii.gz
>
> Using
>
> flirt -in funct0 -r anat -applyxfm -usesqform -omat funct0_2_anat -out funct0_2_anat
>
> resampled the functional to the anatomical and made sure that the mm coordinates
> aligned. I checked this and it looked perfect.
>
> Then I wanted to register the functional data to a standard Talairach template, called tal.nii.gz.
> For that purpose I first registered the anatomical data to this template using flirt and fnirt:
>
> flirt -in anat -ref tal -omat anat2tal -out anat2tal_flirt
> fnirt --in=anat --ref=tal --aff=anat2tal
> applywarp -i anat -r tal -w anat_warpcoef -o anat2tal_fnirt
>
> The resulting anat2tal_fnirt looked very similar to tal. So far so good.
> But now comes the hard part.
> First I combined the two matrices into a single matrix by
>
> convert_xfm -omat funct0_2_tal -concat anat2tal funct0_2_anat
>
> and then I used
>
> applywarp -i funct0 -r tal --premat=funct0_2_tal -w anat_warpcoef -o funct2tal_fnirt.
the anat_warpcoef file has a copy of anat2tal.mat so that is already accounted for. By combining anat2tal with funct0_2_anat you effectlvely ally anat2tal twice.
For your premat you only need to supply funct0_2_anat.
Jesper
>
> The resulting funct2tal_fnirt looked bad.
>
> Using only the linear registration:
>
> applywarp -i funct0 -r tal --premat=funct0_2_tal -o funct2tal_flirt
>
> produced a result that was roughly similar to the tal template. So I guess that
> the combined matrix is OK.
>
> What is wrong with this approach?
>
> Cheers,
> Ed
>
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