Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
Hi Guang,
it still needs the ?h.sphere files as those are used to establish the spherical coordinate system.
cheers, Bruce On Thu, 12 Nov 2009, Guang Zeng wrote:
Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang
Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
Hello, Bruce,
Thanks a lot for your help! I ran 4 commands, and results are shown below:
1. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
2. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sulc 018_S_0425_20060419_CN my_template0.tif
creating new parameterization... processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface /home/m047599/freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... Segmentation fault
3. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh curv 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.curv... Segmentation fault
4. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sphere 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sphere... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
To me, Command 1 and 4 are kind of doing the same thing, right? So I just need to call any one of them, right?
Command 2 and 3 are failed, is it because of my command line? Actually, the results from command 1 and 4 showed that they have computed sulc, do I still need run command 2 and command 3 in the "Prep Step"?
Thanks a lot! Guang
Date: Fri, 13 Nov 2009 08:15:33 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_make_template question
Hi Guang,
it still needs the ?h.sphere files as those are used to establish the spherical coordinate system.
cheers, Bruce On Thu, 12 Nov 2009, Guang Zeng wrote:
Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang
Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_________________________________________________________________ Windows 7: Unclutter your desktop. http://go.microsoft.com/?linkid=9690331&ocid=PID24727::T:WLMTAGL:ON:WL:e...
no, you shouldn't run 2 and 3. sulc and curv are *not* surface formats, so the code dies trying to read them as such On Fri, 13 Nov 2009, Guang Zeng wrote:
Hello, Bruce,
Thanks a lot for your help! I ran 4 commands, and results are shown below:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sulc 018_S_0425_20060419_CN my_template0.tif
creating new parameterization... processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface /home/m047599/freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... Segmentation fault
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh curv 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.curv... Segmentation fault
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sphere 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sphere... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
To me, Command 1 and 4 are kind of doing the same thing, right? So I just need to call any one of them, right?
Command 2 and 3 are failed, is it because of my command line? Actually, the results from command 1 and 4 showed that they have computed sulc, do I still need run command 2 and command 3 in the "Prep Step"?
Thanks a lot! Guang
Date: Fri, 13 Nov 2009 08:15:33 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_make_template question
Hi Guang,
it still needs the ?h.sphere files as those are used to establish the spherical coordinate system.
cheers, Bruce On Thu, 12 Nov 2009, Guang Zeng wrote:
Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang
Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello, Bruce,
Thanks a lot! Now I come to Round. 1,
I use command lines below for reference subject # 1 (base_1) %%%%%%%%%%%%%%% mris_register -curv $FREESURFER_HOME/subjects/base_1/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_1/surf/lh.sphere.myreg0 mris_register -curv $FREESURFER_HOME/subjects/base_1/surf/rh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_rh.tif $FREESURFER_HOME/subjects/base_1/surf/rh.sphere.myreg0 %%%%%%%%%%%%%%%
My question is: For reference subject #2 to #N, where should I write output surface file,
For example, reference subject #2, base_2 Should my command line be A or B? A. mris_register -curv $FREESURFER_HOME/subjects/base_2/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_2/surf/lh.sphere.myreg0 B. mris_register -curv $FREESURFER_HOME/subjects/base_2/surf/lh.sphere $FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif $FREESURFER_HOME/subjects/base_1/surf/lh.sphere.myreg0
Thanks a lot! Guang
Date: Fri, 13 Nov 2009 13:20:42 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_make_template question
no, you shouldn't run 2 and 3. sulc and curv are *not* surface formats, so the code dies trying to read them as such On Fri, 13 Nov 2009, Guang Zeng wrote:
Hello, Bruce,
Thanks a lot for your help! I ran 4 commands, and results are shown below:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sulc 018_S_0425_20060419_CN my_template0.tif
creating new parameterization... processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface /home/m047599/freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... Segmentation fault
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh curv 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.curv... Segmentation fault
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% mris_make_template lh sphere 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_0425_20060419_CN (1 of 1) reading spherical surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sphere... curvature mean = 0.000, std = 1.000 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.inflated.H... curvature mean = -0.000, std = 0.602 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.sulc... curvature mean = -0.016, std = 1.234 computing parameterization for surface ../freesurfer-install/freesurfer/subjects/018_S_0425_20060419_CN/surf/lh.smoothwm... writing updated template with 1 subjects to my_template0.tif...
To me, Command 1 and 4 are kind of doing the same thing, right? So I just need to call any one of them, right?
Command 2 and 3 are failed, is it because of my command line? Actually, the results from command 1 and 4 showed that they have computed sulc, do I still need run command 2 and command 3 in the "Prep Step"?
Thanks a lot! Guang
Date: Fri, 13 Nov 2009 08:15:33 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_make_template question
Hi Guang,
it still needs the ?h.sphere files as those are used to establish the spherical coordinate system.
cheers, Bruce On Thu, 12 Nov 2009, Guang Zeng wrote:
Hi, there,
I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep".
"The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference."
Here, I listed my script for this "Prep" step please let me if it is correct:
mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif
mris_make_template rh smoothwm sample_0 my_template0.tif
mris_make_template rh sulc sample_0 my_template0.tif
mris_make_template rh curv sample_0 my_template0.tif
Thanks a lot!
Guang
Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Guang Zeng