my question was to do with whether matt's mapping would work well when the surface was made from 300um and scaled, but the ribbon was upsampled to 250um and the rest of the data was 250um.
Like you say, best go with 500um. that's a valid downsampling of 250um that preserves raw diffusion volume properties too. I'm sure it'll be a huge pain at 500um as well :) but faster. On 16 July 2012 18:00, <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: linear surface transforms (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <do...@brainvis.wustl.edu> > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Cc: > Date: Mon, 16 Jul 2012 09:18:37 -0500 > Subject: Re: [caret-users] linear surface transforms > The honest answer to most of these questions is "I don't know"; however, > see inline comments below for any hints I think are worth sharing. > > > On Jul 15, 2012, at 7:56 AM, Colin Reveley wrote: > > > Before I begin something that's going to be tough, may I just confirm: > > > > I've got a structural and other (diffusion related) volumes, all in > register, at 250um. > > > > I need to make wm and pial surfaces in freesurfer, average them, and > then map the structural (myelin) and diffusion stuff using matt's technique. > > > > the trouble is that these volumes don't fit in 256x256x256. they are 330 > long. > > > > so to make FS surfaces I need to downsample the structural from 250um to > 300um > > > > there would then be a Flirt matrix that moved this back to the original > voxel dimensions and volume dimensions. > > > > my question is: once I've downsampled the volume and made the FS > surfaces (and thickness, curv metrics and ribbon volume) > > You'll probably have to multiply your thickness maps by the appropriate > scalar. > > Curvature won't be affected, I don't think. Ditto for sulc, if you use > that. > > > can I use the Flirt matrix to move the FS surfaces back into the > original voxel size, and also transform the thickness, curv metrics and > ribbon volume as being 250um not 300? > > > > I know I can rotate and scale the surfaces in space, so they work with > caret. and I can transform so that 1mm becomes 300um (just a matter of > changing units) . > > > > but can I then transform from 300um to 250um ? > > > > that's not the same as just calling 1mm some other unit. There is an > actual difference in the relation of node to voxel in changing from 300 to > 250. > > You can always apply an affine transform to the surface (either in the GUI > or command line), but you know that, so I guess I don't understand your > question. > > > will the thickness and curv metrics, and the ribbon volume, upsampled > from 300 to 250 still work with the surface meshes made from 300 data, in > the myelin mapping system? > > > > the motivation here is to get as close to a surface made from 250um data > as possible, and to map the 250um data which is detailed. > > > > if it's not going to work, I may as well just down sample everything to > 500um and keep it there. This will be faster and easier, but less detailed. > > Maybe try it the easy way and see if the results look sane. You might > learn something that makes you less inclined to do it the harder way (e.g., > it's not going to work no matter which way you do it). If it works, but > you'd like finer resolution, then sweat these issues. > > > > > 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
