Friday, March 28, 2014

connectome workbench: working with volumes

I think of plotting surfaces when I think of the Connectome Workbench, but Workbench can do quite a few nice things with volumes as well. If you haven't already read my previous HCP tutorial posts, read those first, because I'm going to be skipping quite a bit of the introductory info. I'm using the most recent version of the Workbench, 0.84.

I'm very pleased with these screenshots in this post and will describe how I made them. The pictures show both a surface and volume-slices view of the accuracy map resulting from my searchlight demo.

Before firing up the Workbench, you'll need both the volumetric (NIfTI) and surface (*.shape.gii or *.funct.gii) versions of the file you want to plot, plus the corresponding anatomical underlays. In this case, the demo searchlight accuracy map is aligned to the MNI anatomical template, so we'll use the atlas_Conte69_74k_pals anatomy, as before. Thankfully, the atlas download includes both surface and volumetric versions, so that's ready to go. The demo volumetric NIfTI can be downloaded here, and the wb_command -volume-to-surface-mapping program will create the corresponding *shape.gii file, also as before.

Now that we have all the files we need,we can plot them in Workbench. I started a new .spec file based off the Conte69 anatomy so that I could skip loading the files I didn't need (e.g. borders) and save the ones I do need, but that's not essential (see here for explanation).

Once Workbench is open, we need to load in the images, both volume and surface, that we want to overlay, plus the volume anatomy, since that isn't included in the default Conte69_atlas-v2.LR.32k_fs_LR.wb.spec. These four files (searchlightAccuracies_rad2.nii.gz, Conte69_AverageT1w.nii.gz, searchlight_right.shape.gii, and searchlight_left.shape.gii) can all be loaded (as Volume Files and Metric Files) through repeated use of the File -> Open File dialog.

Finally, we can start making nice pictures. I found it convenient to work with just two Workbench tabs, one for the surface and one for the volume version of the dataset. You can close extra tabs by clicking the little red boxes at the top of each, and open new ones with File -> New Tab.

Go to the first tab and click the "All" radio button in the "View" part of the Toolbar. The window will change to show the surface of both hemispheres, but not the searchlight map; change the bottom two METRIC entries in the Overlay ToolBox to searchlight_right.shape.gii and searchlight_left.shape.gii. You can turn the brain around with the mouse to see the overlay (adjust the color scaling via the little wrench icon). Now, switch the top dropdown box to VOLUME searchlightAccuracies_rad2.nii.gz. This will plot the volume data inside the surface, projected onto planes (twist the brain around to see the planes). You can adjust the planes' location in the "Slice Indices/Coords" part of the Toolbar.

Go to the other tab and click the "Volume" radio button in the "View" part of the Toolbar. Set the bottom dropdown box to VOLUME Conte69_AverageT1w.nii.gz (the anatomic template), then the upper dropdown box to VOLUME searchlightAccuracies_ rad2.nii.gz.When both of these layers are checked On the view should look something like the right side part of this image.

Now we have two tabs open, one with a surface, and one with a volume. To view both side-by-side like in the screenshot, click View -> Enter Tile Tabs. There are a lot of neat things you can do in the "Tile Tabs" view; play around with it and check out the tutorial.

Another feature of the Workbench I really like for volumetric data is making "montages": views of many slices at once, like the top screenshot in this post. To make these, click the "M" button in the "Slice Plane" part of the Toolbar. You can then switch the number of slices shown by adjusting the boxes in the "Montage" part of the Toolbar, and where it starts showing slices in the "Slice Indices/Coords" part of the Toolbar. The montage view doesn't have to be axial slices, but any type - just click the buttons in the Slice Plane part of the toolbar.

So, this was an overview of what I thought was pretty nice when using the Workbench with volumetric images. I did find a few things frustrating, particularly the Yoking; I just couldn't make yoking work. Also, volume-only montage view is rather like MRIcron ... but the view doesn't recenter on clicked coordinates; you adjust the position through the "Slice Indices/Coords" part of the Toolbar. It would also be neat to plot horizontal lines on the surface when viewing data like in the top screenshot, where the horizontal lines indicate the slices shown in the volume montage. But, some nice features, and I'll probably be using the Workbench with volumetric data quite a bit more in the future.

UPDATE (7 May 2014): Tim Coalson told me how to get Workbench to recenter on clicked coordinates: depress the Volume ID button (yellow arrow) in the Information box (red arrow button makes it appear). He said they might make this the default in future versions of Workbench, which would help.

Note that if you click the red-arrow i button again (so it is popped-out, rather than depressed) the Information window won't keep appearing every time you click in the volume.

1 comment:

  1. Thanks so much! Have been working with Connectome Workbench for a while now and could never work out how to get a nice montage (always resorted to screenshotting FSLView). Followed through your tutorial and I have it now, much better than fslView. Thanks again!