I was able to successfully use multimodal registration to register some of our pediatric DTI data to PAM50 template and extract the WM tracts from there. However, that’s not the case when trying to register the spinal cord injured DTI data (specially with motor complete impairment cases).
I have tried different routes and options (i.e. corrected the cord mask manually to account for cord atrophy/lesion and then used the manual corrected segmentation as an input for the registration). I have also tried different algorithms in the param section.
The outcome of registration is the distorted cord at the site of injury.
I was wondering if you have any recommendation on how to treat the non-healthy cords at the time of registration?
I appreciate your help in advance,