Hi Doug,
   With the terminology in the document you provided, I can summarize what I want to do exactly as part of the flow chart in page 7. I listed it as between==. As described in the document, I can get Ta, Tb by <mri_info –vox2ras-tkr vol>; and R from a file <register.dat>; am I right?  Practically, I may put my template as a subject a0, and individuals as subjects a1, a2 ..., an. What is the file name of [Vol A TkReg "RAS"] under the subject folder?
==============
   [Volume A CRS] -> (Ta) -> [Vol A TkReg "RAS"] <- (R) <- [ Vol B TkReg "RAS"] <- (Tb) <- [Volume B CRS]
==============
Thanks a lot.


On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Peng, there's a lot going on there, and it is not specific enough for
me to make recommendations. Take a look at the docs we have on our
coordinate systems

http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf

you might get the answer you need from there or at least use our
terminology to point me in the right direction

doug




On 03/10/2014 12:20 PM, peng wrote:
> Thanks Doug for your reply. In fact I need both. I do this mainly for
> computation (in volume); and display (in surface) is also cool.
>
> The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in
> volume of the template (icbm152). This can be implemented as an Nx3
> matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in
> the volume.
> RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3
> dimensions are taking right, anterior, superior as positive, e.g
> An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior
> and nz0 mm superior of AC.
> The above two systems can be easily transformed by a transformation
> matrix.
>
> I wish to know the correspondent locations of An in individual
> subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish
> to find the center of V1 in the subject as B1.
> So far, all the locations are represented in volume. However, I guess
> to normalise the individual brain to the template, freesurfer will
> extract the volumes to surfaces. I imagine the procedure will be like
> An (volume representation of dots in template)  -> ASn (surface
> representation of dots in template) -> BSn(surface representation of
> dots in individual) -> Bn(volume representation of dots in
> individual). If this assumption is correct, I would like to use Bn for
> my computation and ASn for display later.
>
> I hope I have made myself clearer.
>
> best
> Peng
>
>
> On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     Do you mean you want to display them in the MRI volume or on the
>     surface
>     (or both)? When you say that they are in "RAS coordinates", what
>     do you
>     mean? How are the coords defined?
>     doug
>
>
>
>     On 03/08/2014 07:26 AM, peng wrote:
>     > Dear freesurfers,
>     >
>     >    I have a set of dot locations (300~400) in a template brain,
>     > indicated by indices of a 3-D array of the template MRI data, which
>     > can be easily transformed to RAS coordinates. I wish to project
>     these
>     > dot locations to individual MRIs, ideally also as indicated by
>     indices
>     > in the 3-D array of the individual MRI data. Is it possible to do it
>     > in freesurfer? I guess the surface-based procedure shall work
>     well for
>     > this. It might be a very junior question, if it was documented
>     > somewhere before, please let me know the link. Thank you very
>     much for
>     > help.
>     >
>     > best
>     > Peng
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358
>     Fax: 617-726-7422
>
>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>     www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     Outgoing:
>     ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     The information in this e-mail is intended only for the person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in error and
>     the e-mail
>     contains patient information, please contact the Partners
>     Compliance HelpLine at
>     http://www.partners.org/complianceline . If the e-mail was sent to
>     you in error
>     but does not contain patient information, please contact the
>     sender and properly
>     dispose of the e-mail.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer