Hi Yunxin

can you explain a bit more about what you are trying to achieve? We already provide a tesselated representation of the pial surface. I don't think it will be possible to discretize it into a volume and retesseelate with a fast marching algorithm without giving up lots of accuracy

cheers Bruce

On Wed, 7 Aug 2013, Yunxin Wang wrote:

Hi Bruce, Thanks very much for the explanation. According to your suggestion, I think maybe I should try to figure it out with a 2D fast marching process. I could extract it to a 2 dimension matrix by matlab with FreeSurfer package, right?

Best, Yunxin

2013/8/6 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Yunxin

  could you cc the list so that others can answer? I don't think you will be able to get a reasonable surface out of a
  discretized 256*3 volume for the pial surface. There are many, many places where the pial surface comes within a
  fraction of a mm of itself that you will not be able to represent.

  cheers
  Bruce

  On Tue, 6 Aug 2013, Yunxin Wang wrote:

        Hi Bruce,
        Thanks for your response. Actually I want to use the fast marching toolbox
        to further analyze the pial surface that FreeSurfer has reconstructed
        automatically, but according to the procedure only the pial surface will be
        used for fast marching process and I found out the input file of fast
        marching is a 256*256*256 matlab file which I could just load in matlab but
        couldn't see any detail. Do you think I can use the freesurfer_read_surf
        function in matlab to transfer the surface? 

        Best,
        Yunxin


        2013/8/5 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
              Hi Yunxin

              the surface lives in a continuum and is 2D. Do you mean filling
              the space between the ?h.white and ?h.pial surfaces? We do that
              as part of recon-all and create ribbon volumes in the mri dir
              cheers
              Bruce


              On Mon, 5 Aug 2013, Yunxin Wang wrote:

                    Hi dear all,
                    I'm new here and I've a simple question that how
                    could I transfer the reconstructed pial surface
                    file(like lh.pial) into a
                    256*256*256 matlab matrix used in later fast
                    marching process?

                    Any suggestion will be appreciated!
                    Thank guys.

                    Best,
                    Yunxin Wang






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