Hi Donna, I am so confused - I have been trying to get this right now for 4 days and its just not working. What I need is a brain - a full brain, that I can put some foci on. My coordinates are in taliarch and tournoux space - so if there is a brain out there that I can either get in that space or change my coordinates for another space (like your PALS) that would be fine. However, even looking at your PALS brains all fiducial surfaces are half brains - and since I need to put the foci on a fiducial surface I'm not sure how this is going to work.
I do appreciate your help, but as you can tell this is getting frusterating for me. Thanks, Erin Quoting Donna Hanlon <[EMAIL PROTECTED]>: > Hi Erin, > > Ah, yes: Certainly if you use the version that comes with SPM or FSL, > it won't be, but if you use the one in the AFNI_HOME/src/data directory, > it should be. The @auto_tlrc help says this: > > NOTE: These datasets have been slightly modified > from > their original size to match the standard TLRC > dimensions (Jean Talairach and Pierre Tournoux > Co-Planar Stereotaxic Atlas of the Human Brain > Thieme Medical Publishers, New York, 1988). > That was done for internal consistency in > AFNI. > You may use the original form of these > volumes if you choose but your TLRC > coordinates > will not be consistent with AFNI's TLRC > database > (San Antonio Talairach Daemon database), > for example. > > Donna > > On 12/15/2005 09:13 AM, [EMAIL PROTECTED] wrote: > > >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 > >>>>>[email protected] > >>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>_______________________________________________ > >>>>caret-users mailing list > >>>>[email protected] > >>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > >>>> > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>>---------------------------------------- > >>>This mail sent through www.mywaterloo.ca > >>>_______________________________________________ > >>>caret-users mailing list > >>>[email protected] > >>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > >>> > >>> > >>> > >>> > >>> > >>_______________________________________________ > >>caret-users mailing list > >>[email protected] > >>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> > > > > > > > > > >---------------------------------------- > >This mail sent through www.mywaterloo.ca > >_______________________________________________ > >caret-users mailing list > >[email protected] > >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > ---------------------------------------- This mail sent through www.mywaterloo.ca
