Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly.
doug

Bruce Fischl wrote:

Hi John

Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface.

cheers
Bruce
On Wed, 7 Dec 2011, John Griffiths wrote:

[ Douglas and Dan - sending this again as I didn't sent it to the list
address before. Sorry.  ]

Thanks guys.
 When I run mri_info on the .mgz file I was using before it seems crash
(nothing happens, and have to press ctrl+c to get the console back). So I
suppose that partially explains mri_surf2surf not working. Not sure what's
going wrong there - the command I used was
     mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial
     /home/jdg45/lh.pial_converted.mgz

For the original question - I was using a converted .mgz file because when I
just give it the path to the 'lh.pial' file in the same directory it says it
cant determine the file type -
     mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval
     /work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval
     /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282
Standard output:
ERROR: could not determine type of
/work/imaging5/Freesurfer/CBU070282/surf/lh.pial
Standard error:

Is there a .xxx suffix for those files I should be using?
Incidentally, the reason I'm doing this is that I want to downsample a
surface file; someone suggested to me to use mri_surf2surf with the
'trgicoorder' flag. Is this a good way to downsample a surface?
Thanks,
john


On 6 December 2011 19:02, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

     surf2surf actually takes surface overlays (not surfaces
     themselves) as input, and they can be in any format that FS
     reads. The wiki is probably not up-to-date as those options are
     ok.
     doug

     Daniel Wakeman wrote:
           Hi John,

           It seems weird that you are using .mgz files (this
           suffix is for
           volume files) with mri_surf2surf (whose inputs
           should be surfaces).
           Also, it seems that several of the options you are
           trying I don't
           believe exist at least according to the wiki (e.g.
           -cortex -fwhm). Are
           you sure you are using the right command?

           D

           On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths
           <j.davidgriffiths@gmail.com> wrote:
                              Dear list,

                 I am having the following memory
                 allocation problem when running
                 mri_surf2surf. Can't find any mention of
                 this error on the list or the
                 internet - sorry if I've missed
                 anything.

                 mri_surf2surf --cortex --fwhm 5.0000
                 --hemi lh --sval
                 /home/jdg45/lh.pial_converted.mgz --tval
                 /home/jdg45/CBU070282_smoother_surf.mgz
                 --s CBU070282
                 Standard output:
                 srcsubject = CBU070282
                 srcval     =
                 /home/jdg45/lh.pial_converted.mgz
                 srctype    =
                 trgsubject = CBU070282
                 trgval     =
                 /home/jdg45/CBU070282_smoother_surf.mgz
                 trgtype    =
                 srcsurfreg = sphere.reg
                 trgsurfreg = sphere.reg
                 srchemi    = lh
                 trghemi    = lh
                 frame      = 0
                 fwhm-in    = 0
                 fwhm-out   = 5
                 label-src  = (null)
                 label-trg  = lh.cortex.label
                 OKToRevFaceOrder  = 1
                 Reading source surface reg
                 /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg
                 Loading source data
                 Standard error:
                 MRIalloc: could not allocate 2032167524
                 slices

                 Cannot allocate memory
                 Return code: 254


                 Any suggestions?


                 Thanks,
                                 john

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html