Getting started with Connectome Workbench 1.4.2

Here is an updated version of my introductory tutorial for the Connectome Workbench, written for Workbench 1.4.2. This new version of Workbench has some nice features (only a few of which are described here!), so I suggest you try this one rather than a previous version. I have a few other posts on Workbench and HCP-related topics, mostly linked from the "Connectome Workbench: 1st steps" post.

downloading the program

Connectome Workbench has versions for Windows, Mac OS, and Linux; just click the download link for your OS (Linux types can also install Workbench via NeuroDebian).

On Windows and Mac you don't "install" Workbench, but just unzip the download then double-click the executable. On my windows box I put the download into d:\Workbench\, unzipped it, and got a bunch of subdirectories. Navigate through until you find wb_view; in my case it's at D:\Workbench\workbench-windows64-v1.4.2\bin_windows64\wb_view.exe. Double-click wb_view to start the program. If you don't want to navigate to this directory each time to start Workbench, make a shortcut to wb_view.exe and put it on your desktop or in a handy menu.

Aside: wb_command.exe is in the same directory as wb_view.exe. wb_command.exe is not a GUI program (nothing much will happen if you double-click it!), but is useful for various functions; see this post and this documentation for more.

getting images to plot

Workbench doesn't come with any images, so this tutorial will use ones from my knitr tutorials, available at https://osf.io/w7zkc/. Download all of the files under "knitr tutorials", the "surface (GIFTI) brain plotting" and "volumetric (NIfTI) brain plotting" subdirectories. (The .rnw files should be kept in separate directories if you're going to compile the knitr tutorials.)

Aside: Only the files from the osf site are needed for this tutorial, but you will likely want more anatomic underlays than these. I suggest underlays from the HCP S1200 release for volumetric (MNI) and fsLR surfaces; I converted the fsaverage5 surfaces from our local FreeSurfer installation, but FreeSurfer provides many more than the pair I put into osf.

seeing blank brains

Open the Workbench GUI (e.g., by double-clicking wb_view.exe). A command window will open (just ignore it), as well as a interactive box prompting you to open a spec or scene file. Click the Skip button to load the main program. Note: spec and scene files are very useful, and a big reason to use Workbench, because they let you save collections of images and visualizations, which can save a massive amount of time. I won't cover them in this tutorial, though.

Since we skipped loading anything, Workbench opens with a blank screen. We want to first open images to use as underlays: a NIfTI volumetric underlay to plot volumetric blobs on, and GIFTI surface files to plot surface blobs on (see this post for a bit more about file types).

Select File -> Open File from the top menus to open a standard file selection dialog. Navigate to where you put the images from "surface (GIFTI) brain plotting", and change the Files of type drop-down to "Surface Files (*.surf.gii)", then select and open the four fsaverage5 .surf.gii files (two hemispheres * two inflations). Open the Open File dialog again, navigate to where you put the files from "volumetric (NIfTI) brain plotting", and set the Files of type drop-down to "Volume Files (*.nii *.nii.gz)", then select and open S1200_AverageT1w_81x96x81.nii.gz.

Aside: Connectome Workbench works with both fsLR and fsaverage5 surfaces (the two types in the gifti tutorial files), but not at the same time.

All of the underlay images are now loaded in Workbench, but we need to tell it to display them like we want: let's put the surfaces on the first tab and volumes on the second.

The above images show the settings to display the volumes and surfaces (click to enlarge). The first tab probably was already set for multiple surfaces ("Montage"), and likely now shows four wrinkly (pial) brains. Since both pial and inflated fsaverage5 surfaces were loaded, which are shown where can be adjusted with the Montage Selection part of the toolbar (highlighted in red). Try adjusting how many and which surfaces are viewed by changing these settings. You can click and drag the hemispheres around with the mouse; use the buttons in the Orientation part of the menu to reset.

Click on the second tab (probably labeled "All"), then choose Volume in the View part of the menu (circled in red above). The top menus and tab title should change, and a single slice of the volume be displayed. Try adjusting the number and spacing of the volume images. For example, show more slices by clicking the Montage On button (right red arrow), and adjust the image arrangement with the values in the Montage menu boxes (left of the vertical red line). The height of the slices is changed in the A: (axial) box of the Slice Indices/Coords menu (right of vertical red line). The crosshairs can be turned on and off with the button at the bottom left of the Slice Plane menu (left red arrow); the labels on and off with the adjacent LARP and XYZ buttons.

adding overlays

Now that we have arranged underlay images, let's add something on top. Overlays are opened in the same way as the underlay images, via File -> Open File. The Open File window is probably still in the nifti tutorial directory and set to Files of type "Volume", so select the two images in that directory that are not already loaded: continuousOverlay.nii.gz and Schaefer2018_400x7_81x96x81.nii.gz. Workbench won't show the overlays right away, but don't worry - they were opened.

To load the surface overlays use the File -> Open File menu option again (it doesn't matter which Workbench tab you're on), navigate to the directory with the gifti tutorial files, and change the Files of Type: box to "Metric Files (*.func.gii *shape.gii). Select the two fsaverage5 files (fsaverage5_STATS_L.func.gii and fsaverage5_STATS_R.func.gii) and click Open.

Workbench will pop up a query box like this, one for each hemisphere. Select the matching Cortex for each file, and click OK. As with the volume overlays the appearance of Workbench won't change, but the files were read.

To see the images we just loaded, we need to turn the proper overlay layers “On” the surface and volume tabs. The Overlay ToolBox settings control the loading and appearance of the overlay images and work similarly for surfaces and volumes.

On the surface (Montage) tab select the two overlays (one for Left and one for Right; order does not matter) in the File boxes, then click the rows On, as pointed out by red arrows. The color scaling is rather mysterious, but just leave it for now.

These STATS overlays were generated by an afni GLM, and contain multiple named slots. Which statistic is displayed on each hemisphere can be controlled by the Map boxes highlighted in green (note that this number is 1-based while afni uses 0-based, so the numbers shown with 3dinfo are one less). While Workbench lets you show different maps (statistics, in this case) on each hemisphere, it's more usual to want to see the same map on both hemispheres. The Yoke options (between the red and green arrows) will link the two hemispheres together: switch both from "Off" to "I", and when you change one hemisphere's map the other should as well.

On the Volume tab, note that the last row in the Overlay ToolBox is S1200_AverageT1w_81x96x81.nii.gz, the anatomic underlay. This is good - we want to have the anatomy under the overlays. Select one of the volumetric overlay files in each of the other rows using the File dropdown menu (red arrows), and click them On and off.

The two volume overlays in the tutorial dataset are 3d - only one image, rather than 4d (3d plus time or statistics) - so the Map and Yoke options are disabled. Workbench used greyscale for the overlays, but if you look closely and click the layers On and off you can see that the layers are in the order of the Overlay ToolBox File rows: Schaefer (parcel mask) on top, then the continuous image (speckly), then the anatomy. Change which file is listed in each row to change the stacking.

change the color scaling

Schaefer2018_400x7_81x96x81.nii.gz is the Schaefer 400 parcel x 7 network parcellation; let’s add some colors to the parcels. On the Volume tab and click the continuousOverlay.nii.gz layer off, so that only the Schaefer parcels are shown on the anatomy. Now click the wrench button in the Schaefer layer's row (green arrow below); the Overlay and Map Settings window should appear.

Change the settings in the window to match this image and see how the histogram and brains change. The histogram at the right shows the range of the data (1:400 for the Schaefer 400x7), how many voxels with each value, and what color they're assigned with the current color palette and scaling settings. In this case we can see that lower-numbered parcels are given greens, and plotted on the left hemisphere. Switch through the different Palettes and range options to see how the appearance shifts.

What if we like this coloring, but only want to show the right hemisphere parcels? The settings below are one way to accomplish it; try switching the Show Data Inside Thresholds and Show Data Outside Thresholds selection to show the left hemisphere.

Click the Close button at the lower right to close the volume's Overlay and Map Settings window, and switch to the surface tab. Show Map 3 ("ON_BLOCKS#0_Tstat") on each hemisphere, then click the wrench in one of the overlay's rows to open the Overlay and Map Settings window again (I clicked the one for the right hemisphere). You'll see that the histogram looks quite different: the t statistics are both positive and negative, roughly normal, with a lot of values around 0.

Can you make it show only values above 1 and below -1, using a typical warm colors for positive, cool for negative scheme, with red and blue corresponding to 1 and -1, respectively? Below is one solution.

Note that only the right hemisphere has the coloring scheme - since I started by clicking the wrench in the right hemisphere's row. I could close this Overlay and Map Settings window, then click the wrench in the left hemisphere's row and set everything again, but there's an easier way: click the Apply to Files button (green arrow) to open the Copy Palette Color ... window, then click both fsaverage5_STATS Metrics on. Click OK, then Close. Both hemispheres should now have the same coloring scheme.

Finally, switch through the different surface Maps - they will have have the new coloring scheme. This happened because the Apply to All Maps option (just above the green arrow in the previous picture) was checked in the Overlay and Map Settings window. If you uncheck this option, changes will only affect the Map you have shown when the wrench was clicked.

parting comments

This tutorial introduces some basic Workbench functionality, but it has many, many more features. The Workbench tutorial is a good next step to see what else it can do. Good luck!