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Importing FreeSurfer Segmentations in BrainVoyager

It is possible to perform automatic cortex segmentation, advanced segmentation and deep neural network (DNN) segmentation in BrainVoyager (see the Users Guide for more information: https://download.brainvoyager.com/bv/doc/UsersGuide/Segmentation/Overview.html)

However, for certain analyses a BrainVoyager user might be interested in performing cortex segmentation in FreeSurfer and import the segmentation results back into BrainVoyager. 

The following document will shortly outline the basic steps involved in exporting volumetric data from BrainVoyager, using the exported data in FreeSurfer for the segmentation pipeline and re-importing the results back into BrainVoyager.

 

Exporting a VMR to NIfTI

  1. Please open your VMR in BrainVoyager and save it as a NIfTI file to your FreeSurfer subject folder:

     

 

Using the exported NIfTI in FreeSurfer

  1. Run the recon-all pipeline in FreeSurfer:

     

  2. After the recon-all pipeline has finished successfully, the results can be re-imported into BrainVoyager. There are different options that can be used to import the results into BrainVoyager.

Import the binary FreeSurfer surface files into BrainVoyager (the default import option)

  1. Please go to Meshes -> Import  Mesh -> Binary FreeSurfer File and select the surface reconstruction that you are interested in, as for example the reconstruction along the white matter boundary, i.e. /sub-01_ses-04/surf/rh.white. Save the rh.white.srf file as sub-01_ses-04_T1w_WM_RH.srf using the menu item Meshes -> Save Mesh As. In the screenshot below you can see the result of the imported FreeSurfer surface.
  2. Repeat the steps for the other hemisphere (/sub-01_ses-04/surf/lh.white)

Import the FreeSurfer ribbon.mgz file and create meshes in BrainVoyager 

  1. In specific cases a user might prefer to import the ribbon.mgz file from FreeSurfer and create meshes in BrainVoyager based on this information.

  2. Please go to Options -> Import FreeSurfer MGH/MGZ File ...  and select the ribbon.mgz file, i.e. /sub-01_ses-04/mri/ribbon.mgz.
     

  3. The voxel intensities in the file label white matter, grey matter separately for the left and right hemisphere;
    1. Left hemisphere white matter: intensity value of 2
    2. Left hemisphere grey matter: intensity value of 3
    3. Right hemisphere white matter: intensity value of 41
    4. Right hemisphere white matter: intensity value of 42
  4. Use the segmentation tab in the 3D Volume Tools to create four different segmentation files: sub-01_ses-04_T1w_WM_LH.vmr, sub-01_ses-04_T1w_GM_LH.vmr, sub-01_ses-04_T1w_WM_RH.vmr, sub-01_ses-04_T1w_GM_RH.vmr
  5. Use these segmentation files for mesh creation and mesh smoothing.
  6. The screenshots below depict the procedure for the white matter of the right hemisphere:

    1. Open the ribbon.vmr file

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    5. Meshes -> Create Meshes:

    6. Meshes -> Advanced Mesh Smoothing

    7. Meshes -> Save Mesh As..

 

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