Dear FSL-experts,
please excuse me for coming up with an old topic, but I got stuck there.
I tried to transform my ROI files from structural (T1) to diffusion (FA) space applying the following steps:
FLIRT: -in: FA ref: T1 –out: diffusion2structural –omat: diffusion2structural.mat
convert_xfm –omat: structure2diffusion.mat -inverse: diffusion2structural.mat
FLIRT: -in: ROI_structural mask –ref: FA -applyxfm – init: diffusion2structural.mat –dof 6 -out: ROI_diffusion mask
However, the ROIs (marked in red) that were originally placed in the subthalamic nucleus in the structural space (Fig1) look distorted and out of place in the diffusion space ( Fig.2).
Where did I go wrong?
Thanks a lot for your kind support,
Best regards,
Verena
|