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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