Support for the curv format as a target was added to mri_surf2surf in freesurfer v4.0. For your version, you can just exclude the -tfmt curv parameter.
On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote:
ERROR: Cannot select curv as target format.
Thank you, Nick.
Xin Wang
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 21:16 To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map
Can you send along the output text that shows the error?
On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote:
Thank you for your response, Doug. I attached all the commends I modified from Han's note. I worked through step1 & 2. But the step3
is
the problem now. step4 hasn't been tried. I look forward to hearing your suggestions.
Thank you again,
Xin
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 19:12 To: Wang, Xin Cc: Nick Schmansky; Freesurfer Mailing List Subject: RE: [Freesurfer] thickness difference map
What is your cmd line and what is the terminal output?
On Wed, 24 Oct 2007, Wang, Xin wrote:
Thank you very much, Nick. I ran into a problem when I ran the
step
3 of Han's note of thickness repeatability. The --tfmt of mri_surf2surf is curv. The step can not be completed.
Please help me.
Thank you again,
Xin
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 10/20/2007 5:34 PM To: Wang, Xin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] thickness difference map
Xin,
Have a look at this wiki page written by Xiao (the author of the
paper):
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
It describes the procedure for how Figure 2 was created.
Nick
On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
Hello, Group,
We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups?
Thank you in advance,
Xin Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Actually, I think it still needs the --tfmt because it cannot determine that it is a curv file from the name of the file.
doug
Nick Schmansky wrote:
Support for the curv format as a target was added to mri_surf2surf in freesurfer v4.0. For your version, you can just exclude the -tfmt curv parameter.
On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote:
ERROR: Cannot select curv as target format.
Thank you, Nick.
Xin Wang
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 21:16 To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map
Can you send along the output text that shows the error?
On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote:
Thank you for your response, Doug. I attached all the commends I modified from Han's note. I worked through step1 & 2. But the step3
is
the problem now. step4 hasn't been tried. I look forward to hearing your suggestions.
Thank you again,
Xin
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 19:12 To: Wang, Xin Cc: Nick Schmansky; Freesurfer Mailing List Subject: RE: [Freesurfer] thickness difference map
What is your cmd line and what is the terminal output?
On Wed, 24 Oct 2007, Wang, Xin wrote:
Thank you very much, Nick. I ran into a problem when I ran the
step
3 of Han's note of thickness repeatability. The --tfmt of mri_surf2surf is curv. The step can not be completed.
Please help me.
Thank you again,
Xin
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 10/20/2007 5:34 PM To: Wang, Xin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] thickness difference map
Xin,
Have a look at this wiki page written by Xiao (the author of the
paper):
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
It describes the procedure for how Figure 2 was created.
Nick
On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
Hello, Group,
We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups?
Thank you in advance,
Xin Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Xin,
It sounds like you will need to get the newer mri_surf2surf to create the thickness difference maps you want. You can either install the v4.0.1 of freesurfer, or I have posted just mri_surf2surf for you to copy to your existing install. That file is located here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/linux
Copy mri_surf2surf to your $FREESURFER_HOME/bin, and then type:
cd $FREESURFER_HOME/bin chmod a+x mri_surf2surf
You may want to save the old mri_surf2surf somewhere.
Nick
On Thu, 2007-10-25 at 12:25 -0400, Doug Greve wrote:
Actually, I think it still needs the --tfmt because it cannot determine that it is a curv file from the name of the file.
doug
Nick Schmansky wrote:
Support for the curv format as a target was added to mri_surf2surf in freesurfer v4.0. For your version, you can just exclude the -tfmt curv parameter.
On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote:
ERROR: Cannot select curv as target format.
Thank you, Nick.
Xin Wang
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 21:16 To: Wang, Xin Cc: Doug Greve; Freesurfer Mailing List Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map
Can you send along the output text that shows the error?
On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote:
Thank you for your response, Doug. I attached all the commends I modified from Han's note. I worked through step1 & 2. But the step3
is
the problem now. step4 hasn't been tried. I look forward to hearing your suggestions.
Thank you again,
Xin
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 2007-10-24 (星期三) 19:12 To: Wang, Xin Cc: Nick Schmansky; Freesurfer Mailing List Subject: RE: [Freesurfer] thickness difference map
What is your cmd line and what is the terminal output?
On Wed, 24 Oct 2007, Wang, Xin wrote:
Thank you very much, Nick. I ran into a problem when I ran the
step
3 of Han's note of thickness repeatability. The --tfmt of mri_surf2surf is curv. The step can not be completed.
Please help me.
Thank you again,
Xin
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Sat 10/20/2007 5:34 PM To: Wang, Xin Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] thickness difference map
Xin,
Have a look at this wiki page written by Xiao (the author of the
paper):
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
It describes the procedure for how Figure 2 was created.
Nick
On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
Hello, Group,
We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups?
Thank you in advance,
Xin Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Nick Schmansky