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 HolgerThe 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.
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 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.
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 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<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.
is it really entirely gone or is there a little piece of the surface there where Heschl's is? On Thu, 16 Feb 2012, Klein, Holger wrote:
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 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.
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 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<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.
no worries. Not sure about freeview. Ruopeng?
On Thu, 16 Feb 2012, Klein, Holger wrote:
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 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Klein, Holger