Inline replies. Tim
On Sun, Jul 14, 2013 at 12:23 PM, Colin Reveley <[email protected]> wrote: > Hi - I have a few questions about WB functionality and plans for > functionality > > a) what is the position on flatmaps? can these be displayed (e.g. made in > CARET5, saved as "surf.gii", will they work? what if the flat coord file > has fewer nodes than the original mesh, which is fine in caret5) > You can always load any valid gifti surface. I believe we added something that disables rotation when a surface marked as a flatmap is loaded, making it more convenient to view it. I think we are going to try to avoid cut surfaces of any variety in our future studies, but it has been requested by others. > b) there's a nice facility to specify a distance from the white or pial > surface and make an average "laminar approximate" surface at that distance. > > but laminae vary in thickness. If one specified multiple distances from > the WM at different points on the mesh (with ROIs and e.g. a spline) it > could be possible to more accurately follow actual laminar lines in high > resolution MRI. I guess that is more of a thought than a question. It would > be really useful. > If you mean -surface-cortex-layer, it doesn't take a distance, it calculates the placement based on a specified fraction of volume above/below the placement of the new surface (based on the same idea as https://www.sciencedirect.com/science/article/pii/S1053811913003480, but implemented differently). There is also -surface-average you can trick into providing a simple weighted average of a fixed fraction by repeating surfaces. We haven't done much with surface modification/creation commands yet, there isn't one that takes an arbitrary placement metric. c) most importantly: given an FSL BEDPOSTX model, one can "estimate fiber > binghams" and also "Takes precomputed bingham parameters from volume files > and converts them > to the format workbench uses for display." > > in either case: how does one actually do that? what does the display look > like? > It currently uses a temporary file format, so we aren't encouraging people to do this yet. > there is -cifti-create-label and -cifti-convert > -cifti-convert just exports the data matrix of a cifti file as something else so that other software that can't read cifti can still use its data. > if one has a GM/WM segmentation, made by e.g. FAST, how can one generate a > suitable cifti from it to pass to "-estimate-fiber-binghams? > > and does it actually matter to -estimate-fiber-binghams what the labels > (WM or GM) are? does it treat GM labelled regions somehow differently? > > I probably don't want to do that (treat them differently in any way). > No, it doesn't care which actual structures are used, it is just to specify the cifti volume space - it matches this space with the trajectory file to ensure that it doesn't try to render trajectories in the wrong fiber file. Again though, these use temporary formats at present, so I probably shouldn't say how to do it with current commands on the list. > It would certainly be nice to display mean fibre orientations as little > vetors like caret_command -map-fsl etc > The current display has options for displaying the bingham as squashed cones, or the set of all samples as lines (though that gets rather slow). The more interesting display option is using the tractography data to select which orientations to show. > But it seems like there more to this. I can't quite get a grasp on it. I'd > like to have a look. > > The latest stuff is great. Thanks. especially applying flirt transforms to > surfs that's really wonderful. > Glad to see some interest. You can also convert the flirt transforms to a more intuitive format (that you can use directly via matrix multiplication with coordinates) with -convert-affine. You can also use fnirt warpfields on surfaces, though you will need to use their tools to invert them first.
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