Thanks, Rob!
Please bear with me, since I’m new to this. Just to make sure I understand, couple more questions:
Right, but I use msmt_5tt algorithm for the response function estimation, which makes me think that the integrity of 5tt generation will impact virtually every consequent step of the process. Am I correct?
It looks to be in the correct format, with brain tissue sum equal 1 and the non-brain 0. However, I noticed that the subcortical structures (CP, thalamus) were considered “non-brain”, giving me a value of 0 in the deep brain regions. Here is the 5tt image:
If that is the reason, is there a way to resolve this without 5ttedit and manual delineation of the subcortical structures to input into 5ttedit? To generate 5tt, I am using a high resolution T1, after I perform linear registration of it onto my B0. Freesurfer way is not desirable as we are interested in the structures the freesurfer likes to omit from its segmentation (brainstem, midbrain).
Thanks a lot!
Olga