Hi again, It is certainly a beginners question, and probably the code examples given below are not right...
Is there anyone that could advice me how to do this? Thanks so much! Markus 2014-02-01 Markus Gschwind <markus.gschw...@gmail.com>: > Dear all, > > I want to create a surface of a partially altered brain T1 (temporal lobe > cut away by hand). > > I figured out that this would be done with mri_vol2surf. > > This command asks for a register.dat file. > > I think that I can get it using this command: > > SUBJECT_DIR=/Users/FREESURFER > > bbregister --s /mri/brain_T1.mgz --mov > /Users/FREESURFER/mri/brain_T1_ins.mgz --reg /FREESURFER/mri/register.dat > --t1 --init-spm > > I well starts calculation, but suddenly stops and complains that there is > no brainmask /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz > > which makes somehow no sense as the brainmask is in > /Users/FREESURFER/mri/brainmask.mgz of course. > > But I don't find a option to specify the brainmask in bbregister. > > What am I doing wrong? > > Thanks for any help! > Markus > > > >
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