Dear Bruce, 

I tried it again, and it worked out well. Mea culpa - I'm deeply sorry.

Is there a chance to load the patch in freeview? 

Thanks a lot, Holger



2012/2/16 Klein, Holger <klein.holger@googlemail.com>
Dear Bruce,

Command for the patch: label2patch wh lh lh.G_temp_sup-G_T_trans.label PAC

Then I loaded tksurfer with: tksurfer wh lh inflated (pial)

Then I loaded the patch in tksufer with the GUI, but it doesn't show up, respectively everything vanished to black.

Thanks, Holger




2012/2/16 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
what is your command line? That isn't an error - it just detects that the patch isn't flattened and so will show it in the original space. Does it show up?


On Thu, 16 Feb 2012, Klein, Holger wrote:

Dear Bruce, 
The patch (only 16 kb ???) was successfully created via label2patch. But
loading it in tksurfer after having loaded a surface the following error
occured:

% surface not flattened - disabling 2d code...

What am I doing wrong? Isn't there a way via the command mri_vol2surf? What
output format should I use for the surface I create with this command?

Thanks, Holger



2012/2/16 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
     p.s. could you cc the list on your replies so others can learn
     (I did on mine)

     On Thu, 16 Feb 2012, Klein, Holger wrote:

           Dear Bruce, 
           Thanks for your help. I did what you advised me to
           do in freeview. It works,
           but the problem is that an overlay does not
           ameliorate my view on the Heschl
           Gyrus. Thus I am looking for a solution to only view
           the pial surface of
           this certain label without the rest of the brain,
           i.e. just the surface of
           the volume that I created with mri_label2vol.

           Do you have a clue to do that?

           Thanks, Holger

           2012/2/16 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
                Hi Holger

                the file you are outputing isn't a surface,
           it's a surface
                overlay. Try loading the inflated surface then
           load the .w file
                with tksurfer load overlay

                cheers
                Bruce


                On Thu, 16 Feb 2012, Klein, Holger wrote:


                      Dear FreeSurfers,

                      To get a better view on the pial surface
           of the
                      Heschl' Gyri I used the
                      command mri_vol2surf after having created
           the
                      suitable volume with
                      label2vol. My goal is to get the pial
           surface of
                      this single label.

                      My Command is:  *mri_vol2surf --src
           pf_lh_vol.mgz
                      --hemi lh --surf pial --sr
                      creg
                      register.dat --out_type paint --o
           A1surf-lh.w*

                      The output file was created without any
           error, but
                      loading the file in
                      freeview or tksurfer an error occured:

                      *command: tksurfer WH lh A1surf-lh.w

                      *subject is WH*
                      *hemi    is lh*
                      *surface is A1surf-lh.w*
                      *surfer: current subjects dir:
                    
            /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide*
                      *surfer: not in "scripts" dir ==> using
           cwd for
                      session root*
                      *surfer: session root data dir ($session)
           set to:*
                      *surfer:    
           /freesurfer/Kontrollen/A1_Wilts_Heide*
                      *checking for nofix files in
           'A1surf-lh.w'*
                      *Reading image info
                    
            (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)*
                      *Reading
                    
            /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz*
                      *surfer: Reading header info from
                    
            /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz*
                      *ERROR: MRISread: file
'/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf-

                      l
                      h.w'
                      has 0 vertices!*
                      *Probably trying to use a scalar data
           file as a
                      surface!*

                      What am I doing wrong?

                      Any help would be greatly appreciated.
           Thanks in
                      advance

                      Holger





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