Hi Gwaenelle et al.,
Thanks a lot for the very informative conversation. I have been following the steps suggested in this conversation and have got as far as
6) convolve the subsequent warpfield with the halfway .mat to obtain the final warpfield to apply to each native GM image
Would you mind explaining to me how to do this? I don't want to make any silly mistakes at this stage.
I imagine that this is necessary so that the steps taken in the affine transformation from native to halfway space are taken into account in the Jacobian for the modulation in the following step.
Also, would step 7) modulate and smooth - be as simple as
fslmaths Subject1_GM_TP1_MNI -div Subject1_Jacobian_TP1_to_MNI Subject1_GM_TP1_MNI_mod
fslmaths Subject1_GM_TP1_MNI_mod -s 2 Subject1_GM_TP1_MNI_mod_s2
fslmaths Subject1_GM_TP1_MNI_mod -s 3 Subject1_GM_TP1_MNI_mod_s3
fslmaths Subject1_GM_TP1_MNI_mod -s 4 Subject1_GM_TP1_MNI_mod_s4?
Many thanks for any help.
Best wishes,
Sean
|