Recently I saw a paper mentioned this ：

By using the deformation field from nonlinear registration, we can build the correspondence between voxels in the template and each linearly-aligned image.  For instance, for each voxel (x, y, z) in the template image, we can find its corresponding voxel (x + dx, y + dy, z + dz) in each linearly-aligned image, where (dx, dy, dz) is the displacement from the template image to the linearly-aligned image defined by the deformation field. 

 

So, I want to get the deformation field from the template to the linearly registered image(flirt_T1). I tried like this :

flirt -in betted_T1.nii.gz -ref Template_without_skull -omat flirt_transf.mat -out flirt_T1

fnirt --in=  betted_T1.nii.gz --ref= Template_without_skull.nii.gz --aff=flirt_transf.mat --cout=warp_coef -fout=warp_fout

fnirtfileutils --in=warp_coef.nii.gz --ref= Template_without_skull.nii.gz --out=fnirtfileutils_field
invwarp --ref=flirt_T1.nii.gz --warp=fnirtfileutils_field.nii.gz --out=invfield_mni2flirt

I want to know if the ' invfield_mni2flirt' file I got is the deformation field of the image I want from the template to the linear registered image(flirt_T1)?

Best wishes,

ping