thanks, I can indeed generate in the same space I display. and mostly I will thanks for tip. The reason not to is to rotate the brain into the slice plane of the microtome edge that subsequently sectioned it.
in other cases I can present as is, ie no transform of the data. It sounds like I'm best off sticking with the vector.gii in caret for now given that I really don't grasp workbench yet. For the future. cheers, C > > ---------- Forwarded message ---------- > From: Matt Glasser <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 14 Jun 2013 14:25:39 -0500 > Subject: Re: [caret-users] wb FSL fibre volume display > 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 > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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