Hi Donna, Using that average brain would be very nice. I just wanted to make sure that it is in taliarch space.
Thanks, Erin Quoting Donna Hanlon <[EMAIL PROTECTED]>: > Hi Erin, > > In most cases, you'll need to adjust the peaks caret guesses. This page > explains how to "tweak the peaks": > > http://brainvis.wustl.edu/help/peak_tweaking/ > > My guess on the error is that your peaks were set such that some steps > produced essentially null output. If you upload your volume here, I can > provide more specific guidance about how the peaks should be set: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > But for a meta-analysis, segmentation of individual brains doesn't seem > practical. For reporting group results (unless you have segmented every > subject and done the group statistics on the surface, e.g., > http://www.jneurosci.org/cgi/content/full/25/43/9919), it's usually more > appropriate to something like our PALS atlas > (http://sumsdb.wustl.edu/sums/download.do?id=6363278), or as described > previously, show volume foci on an average anatomical brain (e.g., > avg152T1). > > Of course, you may be considering segmentation for a project other than > your meta-analysis, but it seems worth clarifying at this stage. Don't > get me wrong: We strongly encourage researchers to segment all their > subjects and do their analysis on the surface, but we also acknowledge > the work involved with patching both hemispheres for every subject. > Trying to do this across multiple studies compounds the challenge. > > Donna > > On 12/14/2005 08:39 PM, [EMAIL PROTECTED] wrote: > > >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 > >_______________________________________________ > >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
