Re: [Freesurfer] mri_vol2surf visualization problem

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

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/**compliancelinehttp://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.