That is right this is all unsupported. The main reason is that we are going to be making changes to the file formats and don't really want the temp formats propagating themselves too widely. We do hope for the next workbench release (after the one happening imminently) have all this sorted out and have all our diffusion visualization features out there and fully supported.
Unfortunately, however, the particular problem you are encountering won't be solved with the new commands. The only way to get the fibers and voxels lined up (in either caret or workbench) is to generate the fibers in the same space you view them. This is one of the reasons that we have moved the HCP's diffusion data into structural space (at the same sampling resolution as the original data) in today's release. The reason is fibers have precise XYZ coordinates whereas voxels are a grid. These only line up if they are in the same space. Peace, Matt. From: Colin Reveley <[email protected]> Reply-To: "Caret, SureFit, and SuMS software users" <[email protected]> Date: Friday, June 14, 2013 1:40 PM To: "[email protected]" <[email protected]> Subject: [caret-users] wb FSL fibre volume display Hi - I guess this is a question specificially for matt. I have some FSL processed diffusion data. I want to display the mean fibre orientations in "little colored lines on top of a volume" format. fslview does this. it's very common. the problem is that the data is very high resolution. So you really can't see the little lines if you print the image from FSLview. One way around this is caret_command -volume-fsl-to-vector I accept this is unsupported. but it does provide a better display for my needs in that the way the vectors appear on the screen is more configurable and generally makes a better figure. only: that command works and thinks in terms of axial slices and the display is interms of distances above and below the axial plane. this means that in coronal view it can end up looking a bit off. I was wondering: surely workbench now has a neat-o way of displaying fibers? it looks like it does. but how to get the data in there? there is wb_command -estimate-fiber-binghams and wb_command -convert-fiber-orientations since bedpostx does not output ka or kb (or std_dev normally, maybe it does in some circumstances) I presume the former command serves as input to the latter in some way how exactly would that work, to create a nice volume display of fibers in workbench? in particualar, the input to -est-fib-bing requires a label volume. is this a volume of integers? where is the specification of what the CIFTI idenifiers (eg CORTEX RIGHT) actually map to as numbers? generally, is it possible to make a fiber file for display in WB given suitable data, and e.g. a FAST segmantation relabelled to the CIFTI itentifier values? Given my goals as described above, do I even want to be trying this? many thanks, Colin _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
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