Hi Max, does this page give you what you need to know? http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 05/30/2013 08:29 AM, schre...@informatik.hu-berlin.de wrote: > Hi Freesurfers! > > I'd like to load my original Nifti T1 image data (subject.nii) and the > wm/gm-surface coordinate data (for instance lh.pial) in matlab as vectors > in the same coordinate system. > > If I do it in the naive way, > i.e. [x,y,z,1]=[i,j,k,1]*sform' for the Nifti coordinates resp. > freesurfer_read_surf(...) for the surface nodes, > then surface and Nifti appear not to be coregisterred. It looks as though > there would be a spacial shift missing. > Although having tried several matrices I cant figure out which is the one > to choose. > > Inspecting the Data by Freeviewer I observe the same spacial shift, > inspecting it by 'tkmedit subject_id brainmask.mgz lh.pial' everything is > fine. > > Could you tell me, which transform I have to apply to the surface > coordinates? That would be really nice. > > Thanks and best Regards, > Max > > _______________________________________________ > 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.
