Re: [Freesurfer] downsampling white matter surface and converting to .tri

I'll leave this for Doug, but it may be that the target subject has to be fsaverage (which is the only one that is actually an icosahedron)

cheers Bruce On Thu, 8 Dec 2011, John Griffiths wrote:

Hi Bruce. That seems to help - this command runs with no errors

   mri_surf2surf --hemi lh --srcsubject CBU070282 --sval-xyz white
  --trgsubject CBU070282 --trgicoorder 3 --trgsurfval
  white_trgicoorder3 --tval-xyz

But unfortunately the --trgicoorder flag doesn't seem to be doing anything; when I run mris_info on the outputs of this command it says 'nvertices' is the same as the original file, for whatever value of trgicoorder I use. The files are the same size as well.

Any idea why this might be happening?

Thanks,                 john

On 8 December 2011 14:45, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi John

  try adding --tval-xyz so that it knows you want to write out a
  surface.

  cheers
  Bruce

  On Thu, 8 Dec 2011, John Griffiths wrote:

        Dear FS peeps,
         
         
        I am trying to downsample a (white matter) surface
        with mri_surf2surf. I
        also want the output in .tri format.
         
        First problem is that mri_surf2surf doesn't let me
        output in .tri format
         
             mri_surf2surf --hemi lh --srcsubject subj1
        --sval-xyz white
             --trgsubject subj1 --trgicoorder 4 --trgsurfval
             subj1_white_downsampled.tri --tfmt tri

         
        gives me
         
             ERROR: could not determine type of
        temp_surf_white.tri

         
        (that happens with the 'tfmt' flag or not)
         
        The command does work when the output is a .gii or
        .mgh file, but when I
        then try to convert those files to .tri format with
        mris_convert I get the
        error
         
             ERROR: MRISread: cannot read surface data from
        file
             subj1_white_downsampled.gii!

         
        ...which is also the error I get when trying to load
        the file into freeview
        as a surface.
         
         
         
        Any idea what I'm doing wrong here? If there is a
        better way to
        convert lh.white into a downsampled .tri file please
        do tell.
         
         
        Thanks very much,
                                             john
         
         
         
        (p.s. thanks to Dan, Doug, and Bruce for getting me
        to this point...)
         
         

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