Hi Estelle, Could you clarify the "overlapped in the anatomic image" part of your message? To clarify where my confusion stems, typically a cortical surface is generated from an anatomical image. So the entire surface intersects the anatomical image, right? (But certainly not vice versa -- the image contains much more anatomy than just the cortex.)
So, if you map activity onto the surface, then anything that intersected the surface necessarily intersected the anatomy, which was the origin of the surface. For any of the clusters of activity, you can generate the COG. There may be an easier way, but one way is to load the metric as a surface shape file (File: Open Data File: File Type Metric: select your filename; then change filetype to Surface Shape). Then use Surface: Region of Interest: Surface Shape Clusters Analysis. You'll get a report listing the COG for each supra-threshold cluster (enter 0.0 or -99999 for Threshold, if you don't want any thresholding). But I suspect I am not interpreting your meaning of anatomical overlap correctly. Donna On 11/03/2008 09:09 AM, estelle.raffin wrote: > > Hi, > > I am interested in cortical reorganizations in M1 and I wanted to know > if in the "region of interest operations" it is possible to calculate > the COG from a metric map overlaped in the anatomic image? > > > > In advance thank you for your help, > > > > Estelle > > > Message du 28/10/08 17:59 > > De : [EMAIL PROTECTED] > > A : caret-users@brainvis.wustl.edu > > Copie à : > > Objet : caret-users Digest, Vol 61, Issue 10 > > > > > > Send caret-users mailing list submissions to > > caret-users@brainvis.wustl.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > or, via email, send a message with subject or body 'help' to > > [EMAIL PROTECTED] > > > > You can reach the person managing the list at > > [EMAIL PROTECTED] > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of caret-users digest..." > > > > > > Today's Topics: > > > > 1. Re: MNI coordinate - additional information on stereotaxic > > foci (David Van Essen) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 27 Oct 2008 13:12:47 -0500 > > From: David Van Essen > > Subject: Re: [caret-users] MNI coordinate - additional > information on > > stereotaxic foci > > To: "Caret, SureFit, and SuMS software users" > > > > Message-ID: > <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > > Alireza, > > > > To expand on what Donna said, > > > > The foci and foci projection (fociproj) file types in Caret are > likely > > to be useful for the needs that you describe. For example, if you > > enter the center of your ROI as a stereotaxic focus in an > identified > > stereotaxic space, you can then project it to the PALS atlas > surface > > and view it in any of the various other stereotaxic spaces that > PALS > > has been mapped to. You can also view it in volume slices as > well as > > on the atlas flat maps. > > > > You can in addition compare your coordinate data, to the > collection of > > 31,000 stereotaxic foci from 1,000 published studies that we have > > recently added to our SumsDB database and made freely available. > > > > The tutorial document and dataset that Donna referred to > (http://sumsdb.wustl.edu/sums/directory.do?id=6617378 > > ; STEREOTAXIC_FOCI_TUTORIAL/ directory) show how to download, > search, > > and view the existing foci. However, it is still in 'beta-test' > mode. > > I just now replaced the previous pdf document and associated > dataset > > with newer versions that correct various minor errors. If you > started > > taking a look at the previous version, please switch to the > newer one, > > and also let us know if there are persisting glitches or matters > > needing clarification. > > > > We are nearing completion of a separate tutorial document that > > describes how to generate foci files and import them into a 'Foci > > Library' that will be introduced into SumsDB. Stay tuned for an > > announcement regarding that. > > > > David VE > > > > > > On Oct 25, 2008, at 8:41 AM, Donna Dierker wrote: > > > > > Hi Alireza, > > > > > > Sorry for the delayed reply, but you happened to catch us at a > > > workshop > > > on human consciousness; I normally don't work on Saturday, but I'm > > > headed to day 2 shortly. > > > > > > A full reply would take more time than I have, but the short > answer is > > > that I don't think Caret does quite what you want -- yet. I think > > > there > > > is a spatial query under development in sumsdb, but it isn't > quite > > > ready > > > for prime time yet. That said, you might check out the foci > > > tutorial here: > > > > > > STEREOTAXIC_FOCI > > > http://sumsdb.wustl.edu/sums/directory.do?id=6617378 > > > > > > Just scan the PDF; you'll be able to tell if it's useful. > > > > > > Another source to try is here: > > > > > > http://brainmap.org/ > > > > > > While this isn't flat map related, you might still find it useful. > > > > > > One could write a script/program that would find the closest > node on > > > the > > > SPM*/FLIRT/MRITOTAL PALS surface to any given MNI coordinate, > and then > > > lookup the paint attributes associated with that node, but I > don't > > > know > > > of an existing utility that makes it easy. > > > > > > Donna > > > > > > On 10/24/2008 08:35 AM, Alireza Salamy wrote: > > >> Dear Caret experts, > > >> > > >> I have mapped my functional data from SPM5 on flat brain > using latest > > >> version of Caret and now I would like to check some > > >> specific activation(I expected to be among the activations > which has > > >> been mapped on flat brain) like [x,y,Z](MNI coordinate).one > bothering > > >> way would be click on each activation and see if the > coordinate that > > >> comes up in voxel(anatomy) section is the same.but first of > all do > > >> the > > >> [X,Y,Z] coordinate which is reported by voxel anatomy shows MNI > > >> coordinate?second,is there a better way of entering MNI > coordinate > > >> and see the corresponding region to that? lets say > entering[x,y,z] > > >> (MNI coordinate)and see where is that coordinate on the flat > brain? > > >> > > >> Thanks, > > >> Alireza > > >> > > >> > > >> > ------------------------------------------------------------------------ > > >> > > >> _______________________________________________ > > >> caret-users mailing list > > >> caret-users@brainvis.wustl.edu > > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >> > > > > > > _______________________________________________ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > ------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > End of caret-users Digest, Vol 61, Issue 10 > > ******************************************* > > > > > > > > > Estelle RAFFIN, Doctorante, > Service de Medecine Physique et Readaptation > Hopital Bellevue, CHU de Saint Etienne, 42055 Saint Etienne Cedex 02 > Tel: 04 77 12 04 67 > Email:[EMAIL PROTECTED] > [EMAIL PROTECTED] > > > > /Créez votre adresse <http://www.laposte.net> électronique > [EMAIL PROTECTED] > 1 Go d'espace de stockage, anti-spam et anti-virus intégrés./ > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
