David,
> > If you have matlab, you can use the attached script. > > Use the attached file AND > (1) download http://www.martinos.org/~mclaren/ftp/Utilities_DGM/PPPI > (2) change the following 2 lines in the attached file: > > addpath(insertspmpath) > > addpath(insertpppipath) > > (3) create_sphere_image is the command you want to run. It takes several > inputs, (a) template image, (b) VOI name, (c) VOI location, (d) sphere > diameter in that order. > > > For VOI location, you need a list of the x,y,z coordinates. Each coordinate > gets its own row. > > > Sorry there isn't more documentation. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Postdoctoral Research Fellow, GRECC, Bedford VA > Research Fellow, Department of Neurology, Massachusetts General Hospital > and Harvard Medical School > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at (773) > 406-2464 or email. > > > > On Thu, May 12, 2011 at 10:18 AM, Donna Dierker > <[email protected]>wrote: > >> 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 >> > >
create_sphere_image.m
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