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