Please remember to post to the list. Thanks! You cannot do that with mri_vol2surf. You'll have to create a binarization of the white matter, then use mrs_tessellate doug

On 02/03/2014 05:24 PM, Markus Gschwind wrote:

Thank you Doug!

But actually I want to produce a *surface*, not an overlay.

What is the right command for that? It should be a file type surf.w I guess.

Thanks Markus

2014-02-03 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:

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>
> <mailto: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>
>         <mailto: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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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