It would work to provide the image you want to use for the myelin map (i.e. the MTR) and then a volume of ones for the T2. Then format the ribbon volume like a FreeSurfer ribbon file (in terms of the numbers that correspond to particular labels).
Peace, Matt. _____ From: [email protected] [mailto:[email protected]] On Behalf Of Timothy Coalson Sent: Sunday, April 22, 2012 10:49 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] myelin mapping Since what the myelin mapping maps is basically T1/T2, you may be able to adjust your data to be in a plausible range for these values, and then fake the T2 by taking an image that looks like a T1 and dividing it by this adjusted data. As long as your data is not discontinuous at the edge of the ribbon, it should work because myelin mapping ignores voxels outside the ribbon. If you don't have a volume that looks like a T1, you can probably use nearly anything as long as its grey matter is fairly consistent and far from zero. Alternatively, if you have the workbench alpha, its volume to surface mapping now has a ribbon mapping option which uses data from all voxels inside the ribbon, rather than just ones close enough to matter for interpolation, though you will need surfaces that approximate the white and pial surfaces: tim@timsdev:~$ wb_command -volume-to-surface-mapping MAP VOLUME TO SURFACE wb_command -volume-to-surface-mapping <volume> <surface> <metric-out> [-trilinear] [-enclosing] [-ribbon-constrained] <inner-surf> <outer-surf> [-volume-roi] <roi-volume> [-voxel-subdiv] <subdiv-num> [-subvol-select] <subvol> ... This doesn't have the artifact correction code from myelin mapping in it, though that code in myelin mapping is partly based on the kinds of artifacts that show up in T1/T2, and may not apply to your data. Tim On Sun, Apr 22, 2012 at 12:06 PM, Colin Reveley <[email protected]> wrote: hello - I'm interested in using your myelin mapping algorithm, however: I don't have a t1w imgage I don't have a t2w image I don't have any freesurfer data. what do I have? I have, instead, a magnetization transfer ratio image from an ex-vivo sample. and, it's very high resolution (250um). I have a pretty good ribbon made in FAST. I have a caret surface made from a downasmpled 500um of the MTR. while the MTR is maybe not a perfect correlate of GM myelin content, it's pretty good and and it's what I have. I don't have time to go through the freesurfer process for this data. since the resolution is good, in principle it's possible to take the caret surefit surface and expand and shrink it so that I can map the MTR and get some vague gesture at laminar differences in myelin. so far the results of this seems to make some sense, although it's hardly exact. I'd like to apply your algorithm, and it does seem to me that the essential data is there (especially as you've previously given me insturction on how to get a ribbon that's suitable using only FAST). so, in effect, I have a midthickness, the equiv of a T1/T2 (I understand it's not the same, but we don't have time to get T1w and t2w from the sample, which won't behave the same in fixed tissue anyway - the MTR is ok. Someone else other than me has made that determination, so let's accept his view) and pretty much a cortical ribbon. however, the inputs to appropriate caret-command aren't right. even though the data is surely ok as input to the algorithm. and I still want to make use of your smart algorithm to process the data using ribbon, instead of just volume->surface metric making. It may validate, or not, claims of more fine tuned (laminar *related*) info. the laminar possibility is nice, but it's of course all over the place in practical terms of surface mapping, even as the data is there. attach screen (crude, top ctx layers shaved off). clearly it can work. if I knew how to fool caret_command by giving it the right data or "fake" data just so I can take advantage of your work with the ribbon, and the things the you wrote about recently. and that would be a help, and progress. best, Colin _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
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