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, schreibm@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
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