re: that, I left something out; the nodes connected by streamlines to an ROI would ideally not just "make themsleves known" they would color according to the path of the streamline (which is in the niftii volume) in the standard RGB (as in green rostrocaudal, red mediolateral, blue inferiorsuperior) by path midpoint, path mean or whatever. The niftii volume provides the coloring information.
hence, giving quick, accessable clues as to what bundle of fibres might be mediating the putative connection between regions. this global sketch can then be used to guide seeds, waypoint masks and targets for more serious analysis of the DWI data, which you then express as a metric. On 16 December 2011 18:36, Colin Reveley <[email protected]> wrote: > Hi - > > Caret has a feature "metric auto load" intended for tractography data. > Essentially, for each voxel in a volume there's an associated metric. When > you click a surface node, the metric for the node associated with that > voxel is loaded. > > That suits me well, and works well for probabilistic tractography which is > easily expressible as a metric, in terms of caret volume->surface > operations from a niftii volume. > > So, cool. > > But, there is also merit in deterministic tractography from tensors or > ODFs. It gives a global picture more cheaply (in terms of memory and > computation). > > I guess the standard for this sort of thing is trackvis. > > Freesurfer has a command dmri_trk2trk > > what this does is take a DTK/Trackvis .trk file (which is a load of > vectors describing streamlines, fancy those colored visuals you always > see), applies a transform (from FLIRT) to get it into (in this case) the > equivalent voxel to voxel relations as the underlying CARET anatomical > image, and outputs a new trk, but also a niftii of vectors. > > Now is there anyway to take that vector niftii and somehow load it as > connectivity (rather than metric) data? > > If not, similar code may be in CARET already, because of the cocomac > interface. This is different, but not that different. > > It would be useful to many I would think. one would define an ROI of > nodes, and the nodes connected to it by streamlines would make themsleves > known. > > thanks Colin, > > Sussex > > >
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