Re: [Freesurfer] Question about global mean cortical thickness

2017-08-14 Thread Douglas N Greve 
please send error and all terminal output


On 08/14/2017 12:47 AM, Yi, Hyon-Ah wrote:
> Dear FS experts,
>
>
> I met an error when I try to run mris_preproc. Actually i succeeded 
> this command with my own scripts and fsgd files before.
> There are 2groups with one covariates but I keep getting this error 
> like below.
> mris_preproc --fsgd TESTTEST_age_only.fsgd --hemi lh --meas thickness 
> --target fsaverage --fwhm fwhm10 --o lh.thickness_age.s10.mgh
> ERROR: no subjects specified
> I attached my fsgd file.
> This fsgd file was made using emacs.
> Regards,
> Hyon-Ah Yi.
>
>
>
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Re: [Freesurfer] Question about global mean cortical thickness

2017-08-13 Thread Yi, Hyon-Ah 
Dear FS experts, 

TESTTEST_age_only.fsgd
Description: Binary data
I met an error when I try to run mris_preproc. Actually i succeeded this command with my own scripts and fsgd files before. There are 2groups with one covariates but I keep getting this error like below. mris_preproc --fsgd TESTTEST_age_only.fsgd --hemi lh --meas thickness --target fsaverage --fwhm fwhm10 --o lh.thickness_age.s10.mghERROR: no subjects specified
I attached my fsgd file. 
This fsgd file was made using emacs. Regards, Hyon-Ah Yi. ___
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Re: [Freesurfer] Question about global mean cortical thickness

2017-08-13 Thread Bruce Fischl 
By default the white matter, but you can compute the pail area if you want
Cheers
Bruce 

> On Aug 13, 2017, at 8:21 PM, Zhiliang Long <15756307...@163.com> wrote:
> 
> Hi Bruce
>Thanks very much for your suggestion. Just one more question that I am 
> confused with. Is the surface area calculated based on the white matter 
> surface or pial surface ?
>   Thanks for your time.
> 
> Best
> Zhiliang
> 
> 
> 
> 
> 
> 
> At 2017-08-13 22:47:07, "Bruce Fischl"  wrote:
> >Hi Zhiliang
> >
> >the thickness is the average of the min distance from gray-to-white and 
> >white-to-gray at each vertex. The surface area is the average area of the 
> >triangles attached to a vertex (divided by 3 I think).
> >
> >cheers
> >Bruce
> >
> >
> >On Sun, 13 Aug 2017, Zhiliang Long wrote:
> >
> >> Dear FS experts:
> >>  I am writting to ask for help about the computation of global mean
> >> thickness. On the FAQ page, one suggestion is that the global mean 
> >> thickness
> >> is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) /
> >> (lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and
> >> ?h.surfarea are calculated. 
> >> Any suggestions are appreciated.
> >> Thanks for your time.
> >> 
> >> Best
> >> Zhiliang Long
> >> 
> >> 
> >> 
> >>  
> >> 
> >> 
> >>
> 
> 
> 
>  
> 
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Re: [Freesurfer] Question about global mean cortical thickness

2017-08-13 Thread Zhiliang Long 
Hi Bruce
   Thanks very much for your suggestion. Just one more question that I am 
confused with. Is the surface area calculated based on the white matter surface 
or pial surface ?
  Thanks for your time.


Best
Zhiliang








At 2017-08-13 22:47:07, "Bruce Fischl"  wrote:
>Hi Zhiliang
>
>the thickness is the average of the min distance from gray-to-white and 
>white-to-gray at each vertex. The surface area is the average area of the 
>triangles attached to a vertex (divided by 3 I think).
>
>cheers
>Bruce
>
>
>On Sun, 13 Aug 2017, Zhiliang Long wrote:
>
>> Dear FS experts:
>>  I am writting to ask for help about the computation of global mean
>> thickness. On the FAQ page, one suggestion is that the global mean thickness
>> is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) /
>> (lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and
>> ?h.surfarea are calculated. 
>> Any suggestions are appreciated.
>> Thanks for your time.
>> 
>> Best
>> Zhiliang Long
>> 
>> 
>> 
>>  
>> 
>> 
>>
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Re: [Freesurfer] Question about global mean cortical thickness

2017-08-13 Thread Bruce Fischl 

Hi Zhiliang

the thickness is the average of the min distance from gray-to-white and 
white-to-gray at each vertex. The surface area is the average area of the 
triangles attached to a vertex (divided by 3 I think).


cheers
Bruce


On Sun, 13 Aug 2017, Zhiliang Long wrote:


Dear FS experts:
     I am writting to ask for help about the computation of global mean
thickness. On the FAQ page, one suggestion is that the global mean thickness
is equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) /
(lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and
?h.surfarea are calculated. 
    Any suggestions are appreciated.
    Thanks for your time.

Best
Zhiliang Long



 


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[Freesurfer] Question about global mean cortical thickness

2017-08-12 Thread Zhiliang Long 
Dear FS experts:
 I am writting to ask for help about the computation of global mean 
thickness. On the FAQ page, one suggestion is that the global mean thickness is 
equal to the (lh.thickness*lh.surfarea + rh.thickness.rh.surfarea) / 
(lh.surfarea+rh.surfarea). I am wondering how the ?h.thickness and ?h.surfarea 
are calculated. 
Any suggestions are appreciated.
Thanks for your time.


Best
Zhiliang Long___
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