Hi Bruce,

Thank you! The creation of register.data worked perfectly.

Now in order to create the mesh file (I suppose .w) of the altered brain with cut out temporal lobe (brain_T1fin), would this command be OK?

mri_vol2surf --src FREESURFER/mri/brain_T1fin.nii.gz --srcreg FREESURFER/mri/register2.dat --hemi lh --projfrac 0.5 --out FREESURFER/mri/brain_T1fin_surf.w --out_type nifti

...however I get
ERROR: could not determine type of FREESURFER/mri/brain_T1fin_surf.w

And when using output_type 'paint' or 'gii' (without the ' ' ) it is calculating something, but freeview crashes when I try to look at it... Actually I have no clue what the output_type should be...

Thanks so much!
Markus


2014-02-03 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
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.gschwind@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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