Re: [Freesurfer] How to realign a surface in matlab to a realigned parent volume

2015-10-29 Thread Bruce Fischl
Hi Octavian you can read the surface into matlab with read_surf.m, but I think you will need to transform the x,y,z coords of every vertex cheers Bruce On Wed, 28 Oct 2015, Octavian Lie wrote: Dear All, I ran recon-all and generated a brain.mgz and say, lh.pial. I converted brain.mgz to b

[Freesurfer] How to realign a surface in matlab to a realigned parent volume

2015-10-28 Thread Octavian Lie
Dear All, I ran recon-all and generated a brain.mgz and say, lh.pial. I converted brain.mgz to brain.nii, imported the latter to matlab/spm and realigned it to rbrain.nii, generating a transform matrix M=rbrain.reorient.mat. if MM is the header for rbrain.nii, the header O for the original brain.n