Hi Donna, I went through all of the steps and only ended up with half a brain! I'm a little confused and discouraged. I would love to use your template - could I somehow change my taliarch co-ordinates to work with the brain that you guys have in the tutorial?
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 > >>>>>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 > >_______________________________________________ > >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
