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 <a...@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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