How to turn off brain extraction in 5ttgen?

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!

Best
Xinyu

Hello Xinyu

There are options for both of those cases, you can use the flag -mask to provide a user-defined mask or -premasked to indicate that the input is already masked. The documentation page has more information :slight_smile:

Best
Fiona

Oh! I checked the documentation page but somehow overlooked that part.
Thank you very much!

Best
Xinyu