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: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@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:
> >
> > 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: fis...@nmr.mgh.harvard.edu
> >> To: freesurfer...@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
> >>>
> >>> _________________________________________________________________
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