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:


                External Email - Use Caution

        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


        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu

        <mailto:Freesurfer@nmr.mgh.harvard.edu>
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
        <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>




    The information in this e-mail is intended only for the person to
    whom it is
    addressed. If you believe this e-mail was sent to you in error and
    the e-mail
    contains patient information, please contact the Partners
    Compliance HelpLine at
    http://www.partners.org/complianceline
    <http://www.partners.org/complianceline> . If the e-mail was sent
    to you in error
    but does not contain patient information, please contact the
    sender and properly
    dispose of the e-mail.