Hi Markus
the --s option should be a subject name, not a path to a volume
cheers
Bruce
On Mon, 3
Feb 2014, Markus Gschwind wrote:
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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