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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Yea, or leave out the --trgsubject all together or spec fsaverage3 as the target. doug

Bruce Fischl wrote:

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...)

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.