Convert FreeSurfer surfaces to Object Format

Written by Owen Phillips. Email Dr. Katherine Narr if you have any questions. For more information, see the protocols page.

Close up on an Object surface mesh


After Freesurfer has finished running it will output .pial and .white surfaces. You can convert these to object (.obj) format using the following steps. This is useful because .pail surfaces only work in Freesurfer programs.

  1. Download the following pipeline. Convet Freesurfer Surfaces to .obj
  2. You will need to set the two following inputs. The MNC file is the first and is important because it will give the output .obj file it's coordinates in image space. If this is wrong, your surfaces won't line up with your images and it will cause a pain down the line. So it's worth the effort to get right. The pipeline module already has this input set to a .mnc file with 0, 0, 0 coordinates. For the second input, reference your .pial and .white freesurfer surfaces.
  3. Enter the names of the output files in the second module (Ascii to Binary). This module is used so surfaces can be more easily read by brainsuite and MNI Display, however, it won't do anything to change the surfaces.
  4. Below is an image of the what the surface should look like.