Addendum to the previous post:

Can I use lh.orig as the input surface instead of lh.inflated?

Also, I ran the command you suggested (I changed -w flag to 10 and used lh.orig as the input surface):

mris_sphere -w 10 lh.orig lh.sphere_test


However, when  I viewed the output of the intermediate forms, all of them were nearly spherical, only lh.sphere_test0010 deviated slightly from the sphere. Even so, it seems its very hard to capture the unfolding process from the cortex to the sphere. Should I be using some other flags? For instance, if I used -w 1 instead, would this help? Thanks.






From: andrewzhao@live.com.au
To: fischl@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
Date: Fri, 11 Apr 2014 16:20:33 +1000

Great, will give this a try. Thanks for clarifying the command flags. Is it also possible to specify the scale using the flag - scale 1?

> Date: Fri, 11 Apr 2014 01:38:01 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: andrewzhao@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] Intermediate stages of cortical inflation
>
> sorry, it shouldn't say "patch", but "file". We will fix that. I wouldn't
> run it with -n. Without it, it will run until it asymptotes. I would try:
>
> mris_sphere -w 20 lh.inflated lh.sphere
>
> cheers
> Bruce
>
>
> cheers
> Bruce
>
>
> On Fri, 11
> Apr 2014, Xuelong Zhao wrote:
>
> > Thanks for pointing this binary out- I didn't realize the user could access it outside
> > of recon-all.
> > I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I
> > used it in the following format but not sure if this is correct:
> >
> > mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test
> >
> > I want to check that the above command converts lh.org to a sphere in 160 iterations,
> > writes out every 20th iteration and ensures the area is preserved?
> >
> > Also, on the fswiki site:
> >
> > *
> >
> > mris_sphere [options] <surface file> <patch file name> <output patch>
> >
> >
> > I'm not certain if <output patch> is synonymous with output surface? Also, what is the
> > purpose of a <patch file name>? Thanks.
> >
> >
> > > Date: Thu, 10 Apr 2014 11:30:15 -0400
> > > From: fischl@nmr.mgh.harvard.edu
> > > To: xuelongzhao@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
> > >
> > > yes, many of our binaries take the -w <n> flag to write out a snapshot of
> > > the minimization every nth step, including mris_sphere
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu, 10 Apr 2014, Xuelong Zhao wrote:
> > >
> > > > Is it also possible to track the inflation all the way to the sphere? I was hoping
> > that
> > > > I could take snapshots of equi-area intermediate forms as the cortex is unfolded
> > onto
> > > > the sphere instead of stopping at the inflated cortex. Thanks.
> > > >
> > > >
> > > >
> > > > > Date: Wed, 9 Apr 2014 08:31:46 -0400
> > > > > From: fischl@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > > CC: greve@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] Intermediate stages of cortical inflation
> > > > >
> > > > > you can use -w 1 to write out every step in the inflation process and
> > > > > choose what you want. If you want it to preserve surface area during
> > > > > inflation (as opposed to just at the end), also include -scale 1
> > > > >
> > > > > cheers
> > > > > Bruce
> > > > >
> > > > >
> > > > > On Wed, 9 Apr 2014, Xuelong Zhao wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I would like to ask whether it is possible to display different levels of
> > > > > > cortical inflation?
> > > > > >
> > > > > > I have been using the command: mris_inflate
> > > > > >
> > > > > > but the -dist and -n flags do not seem to make that much difference. Also,
> > > > > > if I use fsaverage lh.orig as the input file and using the default options
> > > > > > for mris_Inflate I don't seem to be able to recover the lh.inflated surface.
> > > > > >
> > > > > > Are there any alternative commands to control the level of inflation?
> > > > > > Thanks.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
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