The problem was solved.  I typed the wrong name.  
mris_fill had generated wm.mgz correctly, with the problem that a significant 
portion of white matter was cutted off.  The problem I believe is that the 
resolution or the matrix size of wm.mgz is limited to 256 X 256 X 256, but the 
high resolution data has dimension larger than that.  Is it possible to have a 
wm.mgz larger than 256^3?  Or some kind of trick to make it happen?

Thanks,Xiaomin  
Date: Wed, 10 Dec 2014 11:37:29 -0500
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white

what version of FS do you have? You can try runing it with -pial pial but 
I wouldn't think that is needed. Is the lh.pial in 
/misc/data41/yuex/recon_test/test_DB48/surf/
 
and is it readable?
 
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
 
> Yes, lh.pial exists
>
> Xiaomin
>
>> On Dec 10, 2014, at 10:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> 
>> wrote:
>>
>> it only looks for that if it can't find lh.pial. Does that exist?
>>
>>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>>>
>>> Hi Bruce,
>>> the mris_thickness was looking for ?h.gray file to run correctly.  But no
>>> such file exists.  The freesurfer used is 5.3.  Any ideas?
>>> The command line is: mris_thickness test_DB48 lh lh.thickness
>>> The error: reading gray matter surface
>>> /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
>>>
>>>  MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not
>>> open file.
>>> Thanks,
>>> Xiaomin
>>> ____________________________________________________________________________
>>> From: yu...@hotmail.com
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] thickness from pial and white
>>> Date: Wed, 10 Dec 2014 02:47:02 +0000
>>> Thanks.  I will try mris_fill.
>>> Xiaomin
>>> From: Bruce Fischl
>>> Sent: Tuesday, December 9, 2014 4:31 PM
>>> To: Freesurfer support list
>>> it creates a file in curvature format, yes. Did you try mris_fill for the
>>> wm.mgz? It won't be exactly the same as the one we would generate. You
>>> could use mris_fill to generate the interior of the ?h.white surface,
>>> then use the aseg to remove non-wm voxels I guess
>>> On Tue, 9 Dec 2014,
>>> Xiaomin Yue wrote:
>>>> Thanks very much.  Does this create curvature file?  Again, is it possible
>>> to generate wm.mgz from those files?
>>>>
>>>> Thanks,
>>>> Xiaomin
>>>>
>>>>
>>>>> On Dec 9, 2014, at 4:19 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>>>
>>>>> I think just the ?h.white and ?h.pial
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>>>>>>
>>>>>> What I mean by inputs is the default files the mris_thickness will be
>>>>>> looking for to run correctly
>>>>>> Xiaomin
>>>>>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue <yu...@hotmail.com> wrote:
>>>>>>
>>>>>>      Hi Bruce,
>>>>>>
>>>>>>      Thanks for your response.  What's the inputs to the
>>>>>>      mris_thickness?  I need the wm.mgz to generate the ratio of gray
>>>>>>      vs. white matter.
>>>>>>
>>>>>>      Xiaomin
>>>>>>
>>>>>>      Date: Tue, 9 Dec 2014 09:55:21 -0500
>>>>>>      From: fis...@nmr.mgh.harvard.edu
>>>>>>      To: freesurfer@nmr.mgh.harvard.edu
>>>>>>      Subject: Re: [Freesurfer] thickness from pial and white
>>>>>> the thickness you can generate using mris_thikness. Why do you want to
>>> generate a wm.mgz? I guess you could from the wmparc
>>>>>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>>>>>>>> Hi All,
>>>>>>>>
>>>>>>>> Cortical surface reconstructed using caret from a high resolution MRI
>>> data
>>>>>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly
>>>>>>> using freeview.  My questions are whether it is possible to generate 1)
>>> a
>>>>>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using
>>> ?h.pial a
>>>>>> nd
>>>>>>> ?h.white
>>>>>>>>
>>>>>>>> Thanks very much for your inputs.
>>>>>>>>> Xiaomin
>>>>>>>>>
>>>>>>
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