Hi David, I'm going to assume you want a 3D label/ROI/paint volume, rather than writing the node:scalar pairs to a node_numx1x1 nii volume (or as I sometimes see it written as mgz).
I used this dataset to do it: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 Specifically the MACAQUE/Macaque.F99.RIGHT.DEMO.73730.spec spec file. Then I did: Load scenes Select scene 8. Lewis-VE areas, borders on Flat, Fiducial, VeryInflated (Macaque F99 RIGHT Attributes: Paint: Convert Paint Column to Paint Volume Volume Selection: Space: MACAQUE-F99 OK D/C Overlay/Underlay Volume: Paint primary overlay File: Save Data File: Volume Paint File: Macaque.F99UA1.BOTH.LewisVE00.4dfp.ifh Normally, I'd choose NIFTI over 4dfp.ifh, because the latter is generally only readable within wustl.edu, while the formerly is a broadly recognized standard; however, to my knowledge, the NIFTI standards body has not adopted a standard way to represent ROI index to structure/meaning lookup, much less structure/meaning to color. So until that happens, we are stuck with the two work-arounds we know: * AFNI head into which Caret has inserted a LUT_NAMES tag (but other software like AFNI won't recognize) * ifh, which already had a mechanism for representing index to structure/meaning lookup Since you said nifti or 4dfp.ifh, in this case I recommend ifh, because it stores the lookup. Note that the intensities are off by 2, e.g. where the header says this: region names := 0 LVE00_VOT region names := 1 LVE00_V4 region names := 2 LVE00_TEa_m ... The actuall intensity of the voxels intersecting the LVE00_VOT nodes is 2 -- not 0. So add 2 to all the intensities in the header, and direct all questions to Avi Snyder. ;-) Donna On 05/11/2011 08:58 PM, David Grayson wrote: > > Hey everybody, > > > > I am working on a project generating macaque surface ROIs in caret. I > was wondering if there is a way to generate ROIs in nifti format (or > 4dfp.ifh format) for each node within a paint category. For instance, > I have started generating individual ROIs corresponding to each node > in the LVE00 surface category. However, since I have to do this one at > a time, it really takes a while L. Ultimately we would like to make > comparisons of all the ROIs of many different surface categories. So I > am wondering, is there a way to produce all the ROIs of a paint > category at once, instead of one by one? > > > > Thank you, > > > > David > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
