[caret-users] is it possible to calculate COG from metric data?

Mon Nov 3 09:09:45 CST 2008

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 : caret-users-request at brainvis.wustl.edu
> A : caret-users at brainvis.wustl.edu
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> Today's Topics:
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> 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: <6E5DB047-5E84-4A8D-990E-A3F1B9A0E329 at brainvis.wustl.edu>
> 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
> >>
> >>
> >> ------------------------------------------------------------------------
> >>
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> End of caret-users Digest, Vol 61, Issue 10
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> 

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:estelle.raffin at bvra.univ-st-etienne.fr 
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