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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