Thanks Tim, Matt Matt is right: the problem for me is that the vectors ARE free from voxel venters. I want them anchored to voxel centers, for this purpose of making a figure for a paper. And actually I can't think of a scenario where I would not prefer them anchored to voxel centers.
even when they aren't anchored you can get close to what you want with the vector display parameters in the caret GUI. That code is good stuff. Absolutely everything about caret_command -fsl-volume-to-vector and the vector display in caret was good, other than decoupling from voxel centers, and even that is not bad per se. It crashes under a large load, but it's unsupported anyway. I hope all that stuff propagates into workbench in some way, as you seem to indicate it might. cheers, C On 14 June 2013 22:02, <caret-users-requ...@brainvis.wustl.edu> wrote: > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > caret-users-requ...@brainvis.wustl.edu > > You can reach the person managing the list at > caret-users-ow...@brainvis.wustl.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: wb FSL fibre volume display (Matt Glasser) > 2. Re: caret-users Digest, Vol 115, Issue 6 (Colin Reveley) > > > ---------- Forwarded message ---------- > From: Matt Glasser <m...@ma-tea.com> > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Cc: > Date: Fri, 14 Jun 2013 14:56:32 -0500 > Subject: Re: [caret-users] wb FSL fibre volume display > Hi Tim, > I think workbench and Caret have the same limitations for the particular > issue he is having (namely that the fibres ARE free from voxel centers). > Its possible I misunderstood him though. > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Reply-To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Date: Friday, June 14, 2013 2:21 PM > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Subject: Re: [caret-users] wb FSL fibre volume display > > Actually, it is probably more my area to answer this. Inline replies. > > Tim > > On Fri, Jun 14, 2013 at 1:40 PM, Colin Reveley <cm...@sussex.ac.uk> wrote: > >> 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 >> > > -estimate-fiber-binghams is probably what you want, > -convert-fiber-orientations is for when diffusion processing estimates > binghams directly, which I'm not sure is released yet. > > >> >> 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 >> > > No, they have the same kind of output, but different input. > > >> 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? >> > > There are no fixed numbers, it uses the strings, you just have to generate > a workbench style label volume with those strings as the label names. > However, there are fixed numbers for the freesurfer parcellations of the > corresponding structures, and matt may be able to help you there. > Alternatively, you can just take a white matter segmentation volume and > assign something appropriate to the "true" value (usually 1). > > >> 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? >> > > Strings, not values, and yes, it doesn't care where it comes from, it just > has to match the volume space of the fiber data. > > >> Given my goals as described above, do I even want to be trying this? >> > > I don't see why not. There are a few options in fiber display in > workbench, and the fibers are in free space, rather than realigned to voxel > centers, which sounds like a problem you were having. > > _______________________________________________ caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ---------- Forwarded message ---------- > From: Colin Reveley <cm...@sussex.ac.uk> > To: "caret-users@brainvis.wustl.edu" <caret-users@brainvis.wustl.edu> > Cc: > Date: Fri, 14 Jun 2013 21:23:35 +0100 > Subject: Re: [caret-users] caret-users Digest, Vol 115, Issue 6 > > > 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 <m...@ma-tea.com> >> To: "Caret, SureFit, and SuMS software users" < >> caret-users@brainvis.wustl.edu> >> 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 <cm...@sussex.ac.uk> >> Reply-To: "Caret, SureFit, and SuMS software users" < >> caret-users@brainvis.wustl.edu> >> Date: Friday, June 14, 2013 1:40 PM >> To: "caret-users@brainvis.wustl.edu" <caret-users@brainvis.wustl.edu> >> 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 >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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