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 <gr...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > 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. > >
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