I am curious about the concept of ODF magnitude in fiber tracking, which serves the parameter ‘-cutoff’ in tckgen. In practice, the input of tckgen is better a normalized ODF, which is ranging [0,1] I guess. There are two questions here: 1), does the “-cutoff” mean the same thing no matter with the input of original ODF or normalized ODF; 2) how to compute the ODF magnitude map?
The following commands are my attempts, can you give some advice?
fslmaths 5tt/wmfod_norm_d.nii.gz -sqr 5tt/wmfod_norm_d_2.nii.gz mrmath 5tt/wmfod_norm_d_2.nii.gz sum 5tt/wmfod_norm_d_2add.nii.gz -axis 3 fslmaths 5tt/wmfod_norm_d_2add.nii.gz -sqrt 5tt/magni_odf.nii.gz