Wednesday, August 2, 2017

Getting started with Connectome Workbench 1.2.3

WARNING: This post is out of date; the current tutorial is for Workbench 1.4.2.

This post is a tutorial for getting started with Connectome Workbench 1.2.3. Some of this is an updated version of a tutorial I wrote back in 2013 for plotting a NIfTI image as a surface with Workbench. The information in that post is still fairly current, but the post is awkward as an introduction to using Workbench, since creating surface images from volumes is sort of a side topic when just getting started. If you're using Workbench for the first time I suggest that you start with this post, then explore further (such as these links); Workbench can do quite a bit more than covered in this tutorial (or blog!).


If you're using Linux, you can install Workbench via NeuroDebian, but if you're using Windows or Mac OS you don't "install" Workbench but just unzip the download then double-click the executable. On my windows box I unzipped it into d:\Workbench\, so I double-click D:\Workbench\workbench-v1.2.3\bin_windows64\wb_view.exe to start the program. If you don't want to navigate to this spot each time, you can make a shortcut to wb_view.exe or add it to your path. wb_command.exe is in the same directory as wb_view.exe. wb_command.exe is not a GUI program (nothing will happen if you double-click it!), but useful for various functions; see this post and this documentation for details.

getting images to plot

Workbench doesn't come with any images. The Conte69 atlas is normalized to MNI, and aligned to the HCP preprocessed images. Follow the instructions from this page to obtain the 32k_fs_LR mesh version of the atlas if you'll be using HCP/CCF pipeline images. Unfortunately, I can't provide a direct download link, since the SumsDB failed, but I do suggest you obtain this full atlas if you'll be using Workbench with HCP or MNI-normalized images.

UPDATE (8 August 2017): Tim Coalson kindly suggested that an alternative suitable MNI underlay is the 1200 Subjects Group Average Data; this post describes the files and gives the direct ConnectomeDB download link.

We can obtain useful images from BALSA, which takes the same login account as the ConnectomeDB. I downloaded all files from "The Brain Analysis Library of Spatial maps and Atlases (BALSA) database" study link. Unzip the archive from BALSA into a convenient directory.

seeing a blank brain

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 go to 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; these instructions will walk through the BALSA study images (Conte69 or the HCP 1200 subject group average could also be used). The rough idea is that we need 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 BALSA, and change the Files of type drop-down to "Surface Files (*surf.gii)", then select and open all 8 of them (4 inflations * 2 hemispheres). Open the Open File dialog again, setting the Files of type drop-down to "Volume Files (*.nii *.nii.gz)", and select and open both images.

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 image shows the settings to show the volumes and surfaces (click to enlarge it). The highlighted part of the surface tab (1, left side above) shows the toggles for adjusting the surface view; try dragging the hemispheres around with the mouse, then using the buttons in the Orientation part of the menu to reset. Options in the Montage Selection part of the menu control which version(s) of the surface is shown (inflated, midthickness, one hemisphere or both, etc.).

Click on the second tab, then choose Volume in the View part of the menu to tell Workbench we want to see volumes (marked by red dots on the right side of the above image). When you click the Volume button the menus will change, but you won't actually see anything: unlike surfaces, you have to turn the volumetric underlay on as a Layer in the Overlay ToolBox. The red arrow points at the proper box: select one of the NIfTI images in the third box, and check its little On checkbox. You should now see a single slice. I wanted to see multiple slices, so clicked the On button in the Montage part of the menu (also marked by red dots in the above image). Try changing the settings in the Slice Plane, Montage, and Slice Indices/Coords parts of the menu to adjust the view (which slices, how many, which axis, etc.).

adding overlays

Now that we have underlay images, let's add something on top. The BALSA files we downloaded include multiple files (see their documentation for details), but let's just open one CIFTI file: Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii. Open this file in the same way as we opened the underlay images (File -> Open File), but set the Files of type to "Connectivity - Dense Label Files (*dlabel.nii)".

Workbench won't show the overlay immediately, but its name will be added to the Layers boxes in the Overlay ToolBox part of the window (in all the tabs). Click the box in the On column in its row, as marked by the arrows in the image below (left side); the overlay (in this case, the Gordon parcellation) should now be shown (right side). Note that in the screenshot above the left hemisphere is much more inflated than the right (done via the Montage Selection settings), but the single overlay plotted correctly on both; this is the correct behavior.

Finally, let's add an overlay to the volume. Click on tab 2 (where we loaded the volume underlay), then set the top row in the Layer box to the overlay image and click the On box (marked by arrows in the screenshot below): colored regions should appear in subcortical structures. Why just subcortical? Recall that CIFTI files have "grayordinates": surface (for the cortex) and volume (for the subcortex). Since we loaded a CIFTI file, Workbench plotted each part on the appropriate tab. Also, note that I have the underlay in the bottom row of the Layers box, and the overlay in the top row. Try switching them: the underlay will be plotted on top of the overlay.

WARNING: This post is out of date; the current tutorial is for Workbench 1.4.2.