Hi, @Ursula_Tooley
Thank you so much for your response! It helps me a lot.
However, I was thinking to put the derivatives folder out of BIDS folder like in this post (Raw and derivatives seperation) @effigies and it would be also okay?
Also, you said “any freesurfer output”, do you mean that I should maintain the freesurfer output file structure and format as it is? Could you tell me whether I need to change mgz file format to nii.gz or not?
Thank you so much, sincerely!