Hi MRtrix experts!
I am new to this wonderful tool and trying to put together my own pipeline for generating structural connectome from diffusion data.
During the “5ttgen fsl” step I found that the brain extraction by bet is not ideal. Even though I feed a brain-extracted image as input it is still trying to crop the brain to be even smaller.
I was wondering if it is possible to turn off bet during this step or provide a user-defined mask?
I also tried using 5ttgen freesurfer, which works fine but after browsing through the forum it seems this option is not recommended (indeed the subcortical segmentation is not ideal, but I am not sure if this matters given I am only interested in structural connectome between cortical structures?)
Thank you very much!