Donna and David - thanks for your help... I am working on the SureFit Segmentation and seem to be stuck... First, I was curious about what exactly the Gray and White Matter Peak thing is supposed to do. It seems to me, that both the gray and white matter green blobs are on white matter in my brain. Second, when I try to perform the segmentation I am able to get past the disconnect eye part but get stuck on the disconnect hindbrain. An error message comes up:
Error in c:/caret5_borland/packages/source/vtk42- LatestRelease/CommovtkImageData(3546780):GetScalarPointer;Pixel(-1,-1,0) not in memory Current extent = (0, 72, 0, 178, 0 123) Does this mean anything to you? Thanks, Erin P.S. this program looks like its going to be great! Quoting Donna Hanlon <[EMAIL PROTECTED]>: > Hi Erin, > > As you are probably aware, many people report their coordinates as > talairach coordinates, when in fact their data were registered to > another stereotaxic space (e.g., MNI305, MNI152, 711-2B). So be on the > look-out for such cases, because there is considerable difference in the > bounding boxes of those spaces > (http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml). > > The inline replies below assume you're really dealing with T&T > coordinates, and that you prefer rendering the foci with a slice backdrop. > > One advantage, however, to rendering them on the surface -- possibly a > mildly inflated surface which reveals buried sulci, but doesn't lose too > much detail -- is that you render foci that come from a variety of > stereotaxic spaces (i.e., mix mni152 and true T&T). The trick is to > project the foci using an average fiducial surface that accurately > reflects the stereotaxic space used in the study. Once projected, foci > latch onto a surface tile, so they can be rendered on any configuration > of the surface (fiducial, inflated, flat, or spherical). For a > meta-analysis, this is a really nice advantage. > > A major disadvantage, of course, is that it doesn't work for subcortical > nuclei. > > Donna > > On 12/13/2005 07:03 PM, [EMAIL PROTECTED] wrote: > > >Hi, > > > >I am working on a meta-analysis and would like to use your software to make > a > >3d brain with coloured foci of coordinates I input. > >I am a little confused after reading the manuals/doing the tutorials. > >First, I need to input a brain that I can put foci on in Taliarch & Tournaux > > >coordinates. > > > > > From the AFNI list, I know you're an AFNI user, and any of these > volumes included in your AFNI distribution could be an anatomical volume > backdrop for your volume foci: > > src/data/TT_N27+tlrc.HEAD > src/data/TT_avg152T1+tlrc.HEAD > src/data/TT_icbm452+tlrc.HEAD > > For a meta-analysis, I prefer group averaged MRI anatomicals (i.e., > either of the latter two) to a particular individual's anatomy (N27), > but this is your call. > > >Second, I like the look of the surface and volume display, with the kind of > > >planes crossing each other, but would like it so that it only displays the > >three slices and not the surface part. > > > On the D/C menu, select Surface Miscellaneous and select Drawing Mode: > Hide surface. > > > Is that possible? However, I also > >noticed that the foci function only works on fiducial surfaces? Am I unable > to > >put foci on the surface and volume display? > > > > > Create a foci file as usual > (http://brainmap.wustl.edu/caret/html/file_formats/file_formats.html#cellFile > > -- foci and cell formats are identical), but open it as Foci Files - > Volume (the fourth of the file types listed on the Open Data File > menu). If you don't see this option, you need to get an updated version > of caret here: > > http://brainmap.wustl.edu/pub/john/ > login pub > password download > > Probably all you'll need is the updated binary executable (caret5_exe_* > for your platform) -- not the entire distribution. Put this in your > caret/bin directory and make sure its permissions are set such that you > can execute it (e.g., for Linux, chmod u+x caret5). > > >And I think I could put the foci on but... who knows, I may be asking > >questions later. > >Sorry, kind of new to this fMRI stuff. > > > >Thanks for your help, > >Erin > > > > > >---------------------------------------- > >This mail sent through www.mywaterloo.ca > >_______________________________________________ > >caret-users mailing list > >caret-users@brainvis.wustl.edu > >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > ---------------------------------------- This mail sent through www.mywaterloo.ca
