Re: [Freesurfer] Offset in surface rendering

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Okay, will do. Thanks Doug.

Best, Laura

On Thu, Jun 14, 2018 at 1:16 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

So FS was not used to create the surface? If not, then you need to talk to the nipype people about how their gii interacts with your visualization tool.

doug

ps. Please post the FS list and not to us personally. thanks!

On 06/14/2018 03:51 PM, Laura Jeyaseelan wrote:

...

Hi Douglas,

Thanks for looking into this issue. I was using of nipype which internally makes use of the freesurfer marching cubes implementation mri_mc. This directly converts the nifti image to a gifti surface. The python code is shown below

import nipype.interfaces.freesurfer as fs mc = fs.MRIMarchingCubes() mc.inputs.in_file = './lung.nii.gz' mc.inputs.label_value = 1 mc.inputs.out_file = 'fs_lung.surf.gii' mc.run()

Thanks, Laura

On Wed, Jun 13, 2018 at 8:49 AM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:

How did you convert to gii?


On 06/11/2018 08:09 PM, Laura Jeyaseelan wrote:


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    Hi FreeSurfer Developers,

    I'm attempting to convert a 3D label mask (saved as a .nii.gz
    image) into a surface rendering (saved as .surf.gii).

    /import nipype.interfaces.freesurfer as fs/
    /mc = fs.MRIMarchingCubes()/
    /mc.inputs.in_file = './lung.nii.gz'/
    /mc.inputs.label_value = 1/
    /mc.inputs.out_file = 'fs_lung.surf.gii'/
    /mc.run() /

    The code above does not throw any errors, but there appears to
    be an offset when viewing the surface reconstruction using the
    Papaya viewer on the browser. If I try creating the surface
    using Papaya's companion software Mango there is no offset seen.

    Does anyone have any ideas to trouble-shoot this issue?

    I've attached screenshots to show the difference:

    FreeSurfer generated .surf.gii file viewed on Papaya:


    Mango generated .surf.gii file viewed on Papaya:


    Thanks,
    Laura


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