Thursday, February 8, 2018

Connectome Workbench: making a surface version of a volumeric image

This is a tutorial for making a surface version of a volumetric (NIfTI) image (e.g., a ROI) for visualizing with the Connectome Workbench. This post replaces a tutorial I wrote back in 2013, and assumes a bit of familiarity with Workbench. If you're using Workbench for the first time I suggest that you complete the tutorial in this post before trying this one.

First, a warning: as advertised, the steps in this post will make a surface version of a volumetric image. However, the surface version will be an approximation, and likely only suitable for visualization purposes (e.g., making an illustration of a set of ROIs for a talk). If you have an entire dataset that you want to prepare for surface analysis (e.g., running GLMs), you need different procedures (e.g., SUMA, FreeSurfer). Again, I suggest the directions in this post (wb_command -volume-to-surface-mapping) be used cautiously, for quick visualizations, and accompanied by careful confirmation that the mapping produced a reasonable result.

needed files

Before we can make a surface version of a volumetric image, we need to know what it's aligned to, so that we can pick the proper corresponding surface template. Recall that gifti surface files (*.surf.gii) are sort of the underlay anatomy for surface images (e.g., in my Getting Started post on Workbench we load surf.gii files to get a blank brain), so we'll need gifti surface files that will work with our volumetric image (and to serve as the underlay when we're ready to plot the converted volumetric ROI).

For this demo, we'll use fakeBrain.nii.gz (it should let you download without signing in; this is the same NIfTI as shown in other posts), which is aligned to MNI. One MNI dataset with the necessary surface files is the HCP 1200 Subjects Group Average Data; this post describes the files and gives the direct ConnectomeDB download link.

The HCP 1200 Subject Group Average download contains multiple *.surf.gii for each hemisphere, including midthickness, pial, and very_inflated. We can use any of these for visualization in Workbench, but which we pick for the volume to surface conversion does make a difference in what the resulting surface image will look like. It seems best to start with the midthickness surface for the conversion, then try others if the projection seems off.

using wb_command

The wb_command -volume-to-surface-mapping function does the conversion. wb_command.exe (on my Windows machine; file extension may vary) should be in the same directory as wb_view.exe, which you use to start the Workbench GUI. Don't double-click wb_command.exe - it's a command line program. Instead, open up a command prompt and navigate to the directory containing wb_command.exe (on my machine, /bin_windows64/). If you  type wb_command at the prompt it should print out some version and help information; if not, check if you're in the correct directory, and try ./wb_command if you're on a linux-type system.

Now we're ready: we give the function our input NIfTI (fakeBrain.nii.gz), our surface gifti (S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii), the output file we want it to make (demoL.shape.gii), and the options for it to use (-trilinear). Since surface gifti files are just for one hemisphere, we have to do the command twice, once for each. (I included the full path to each file below; update for your machine.)

 wb_command -volume-to-surface-mapping d:/temp/fakeBrain.nii.gz d:/Workbench/HCP_S1200_GroupAvg_v1/S1200.L.midthickness_MSMAll.32k_fs_LR.surf.gii d:/temp/demoL.shape.gii -trilinear  
 wb_command -volume-to-surface-mapping d:/temp/fakeBrain.nii.gz d:/Workbench/HCP_S1200_GroupAvg_v1/S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii d:/temp/demoR.shape.gii -trilinear  

We now have demoL.shape.gii and demoR.shape.gii, surface versions of fakeBrain.nii.gz, which can be viewed in Workbench (or other gifti-aware programs). Check the surface projection carefully: does the ROI align properly with the anatomy? If not, try a different .surf.gii or fitting option (e.g., -enclosing) in the wb_command call; these can make a big difference.

Below the jump are the surface images from the above commands, plotted on the S1200 midthickness in Workbench.