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
>>>
>>> _________________________________________________________________
>>> Hotmail: Trusted email with powerful SPAM protection.
>>> http://clk.atdmt.com/GBL/go/177141665/direct/01/
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