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Dear List,
 
I first run the recon-all stream using a MPRAGE as input, then bbregister to move other mri-sequences to this MPRAGE. Now I want to transfer the values from these mri-sequences to the surface, so that I can calculate on the surface and perform a group analysis.
 
I tried different input files, but it doesn't work...
 
my command is
 
mri_vol2surf --src /path/to/my/subject --out /path/to/my/output --srcreg ???? --surfreg --hemi ?h --fwmh 1,5
 
I wonder wheather I need an extra step to perform the registration file? Because in my current freesurfer output I can't find an "registration.dat"...
 
Moreover I want to create thalamus/basalganglia/ventricle/amygdala etc masks, and I don't know how to automate this - does anybody know if there exists a command?
 
Thanks for your help!
Best, M