Hey Donald, This is cool. Thank you. I am part of Damien Fair's lab at OHSU, and it looks like at some point we may need to use this and ask you a follow up question about it ;)
David ________________________________________ From: [email protected] [[email protected]] On Behalf Of MCLAREN, Donald [[email protected]] Sent: Thursday, May 12, 2011 10:45 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Generating lots of ROIs at once? 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<http://www.martinos.org/%7Emclaren/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]<mailto:[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<http://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]<mailto:[email protected]> http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
