Hello Antonin, 
GM/WM boundary = thickness. correct me if i am wrong. Shouldn't expanding/shrinking the ?h.white or ?h.pial surface to the correct size and shape help with that? I have moved the position of the ?h.white to capture most of the WM using mris_expand but i haven't been successfully with ?h.pial  using mris_expand because the input and output were identical. Hence, I am looking for a way to do it with ?lh.pial and how to tell recon-all to incorporate my changes. Please correct me since I am still new to this (i.e., using individual recon-all scripts). Thank you. 
Best, 
Paul

On Wed, Jan 11, 2017 at 12:32 PM, Antonin Skoch <ansk@ikem.cz> wrote:
Dear Paul,

I am quite surprised that you were successful to estimate correct GM/WM boundary using this tool. As far as I know and looking at the source code, this tool GLOBALLY moves the position of the specified surface to some amount, so it cannot be used to correct local errors. It is used e.g. for estimating the surface ad the midthickness of the gray matter.

See e.g.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-July/011152.html

Antonin


Thanks bruce for your response. I am trying to expand the pial surface (see
attached image) in order to estimate the GM/WM boundary properly. I have
successfully expanded the white matter but when i tried the mris_expand
scripts for pial surface (mris_expand -thickness lh.pial 0.5 lh.newpial),
the output looked identical to the input. Please can you direct me on how
to successfully achieve this for the pial surface and how to incorporate my
changes (expanded surfaces) into recon-all. Thanks.
Best,
Paul
On Wed, Jan 11, 2017 at 11:37 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Paul
>
> it's hard to answer your questions without knowing what you are trying to
> achieve
>
> cheers
> Bruce
>
> On Wed, 11 Jan 2017, miracle ozzoude wrote:
>
> Hello freesurfer,
>> I have several questions about mris_expand command. I know it can be used
>> to expand or shrink a point on a surface by a fixed amount or distance. My
>> questions are:
>> 1) Can it be used to expand the pial surface? if yes, please can you
>> confirm if this is the right script= mris_expand -thickness rh.pial 0.5
>> rh.newpial. If the script is
>> wrong, please can you give me a directions on how to change it and what
>> new flags to add.
>> 2) When I looked up mris_expand description, -thickness was the only flag
>> displayed. Are there other hidden flags? If yes, where can I find them?
>> 3) After expanding ?lh.white and ?h.pial, what steps of recon-all should
>> i run in other to incorporate my changes? Thank you.
>>
>> Best,
>> Paul

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