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

mri_vol2surf will produce an overlay, not a surface. If you want an overlay, use .nii or .mgh instead of .w or .gii (no need for --out_type) doug

On 02/03/2014 04:33 PM, Markus Gschwind wrote:

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 mailto: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
    <mailto: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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