FreeSurfer: How would i convert a .mgz file to stl/vtk or some other mesh file via command line

[Shannen Lambdin]

I've created a .mgz file from a series of dicom files. Does anyone know how to use command line to confer this file to one of the following formats?

.FSM, .INFLATED, .SMOOTHWM, .SPHERE, .PIAL, .ORIG, .STL, .VTK

[camocaze .]

you need to run the full freesurfer pipeline ('recon-all') on your subject. I suggest reading through the online freesurfer wiki so that you understand the basics of how to use the command line tools and set up your directories - there's lots of good documentation for beginners.

once the recon-all pipeline has been completed without errors on your subject, you can convert any of the files in the 'surf' folder into .stl or .vtk using the 'mri_convert' command, i.e.

cd /path/to/subject_freesurfer_output/surf

mri_convert lh.pial lh.pial.stl

mri_convert rh.pial rh.pial.stl

mri_convert lh.orig lh.orig.stl

etc. etc.

hope that helps,

-David

On Tue, Oct 7, 2014 at 6:22 PM, Shannen Lambdin <slamb...@gmail.com> wrote:

I've created a .mgz file from a series of dicom files. Does anyone know how to use command line to confer this file to one of the following formats?

.FSM, .INFLATED, .SMOOTHWM, .SPHERE, .PIAL, .ORIG, .STL, .VTK

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[kruthika kr]

Hi ..

I have processed data output from freesurfer . I need to convert aseg.mgz file to vtk /stl format.
 it is not  possible with mri_convert.Please specify how to do this  ??