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 <gr...@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 > > <gr...@nmr.mgh.harvard.edu <mailto: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 > > <mailto: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 <mailto:gr...@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 > 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 >
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