> Date: Sat, 12 Apr 2014 00:53:34 -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
>
> if it's just for visualization you ca use -i, but in general we just
> project and unfold on the sphere (and don't use -i which inflates and
> drives the surface to the sphere)
>
> On Sat, 12 Apr 2014, Xuelong Zhao wrote:
>
> > I attempted the run again using
> >
> > mris_sphere -w 1 -scale 1 lh.inflated lh.sphere_test
> >
> > However, even with the -w 1 set the intermediate surfaces are all very close
> > to the sphere. Are there any other flags I could try?
> >
> > Date: Fri, 11 Apr 2014 10:25:56 -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
> >
> > yes, that would help
> > On Fri, 11 Apr 2014, Xuelong Zhao wrote:
> >
> > > 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 sphe
> > re. Should I
> > > be using some other flags? For instance, if I used -w 1 instead, would thi
> > s 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 i
> > t 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 a
> > ccess it
> > > outside
> > > > > of recon-all.
> > > > > I've had a look at the fswiki for mris_sphere and it doesn't seem to b
> > e 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? A
> > lso, 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 snapsh
> > ot 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 sphe
> > re? I was
> > > hoping
> > > > > that
> > > > > > > I could take snapshots of equi-area intermediate forms as the cort
> > ex 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 inflat
> > ion
> > > > > > > >
> > > > > > > > you can use -w 1 to write out every step in the inflation proces
> > s and
> > > > > > > > choose what you want. If you want it to preserve surface area du
> > ring
> > > > > > > > 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 differen
> > t 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 diffe
> > rence. Also,
> > > > > > > > > if I use fsaverage lh.orig as the input file and using the def
> > ault options
> > > > > > > > > for mris_Inflate I don't seem to be able to recover the lh.inf
> > lated
> > > surface.
> > > > > > > > >
> > > > > > > > > Are there any alternative commands to control the level of inf
> > lation?
> > > > > > > > > Thanks.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > _______________________________________________
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> > >
> > >
> >
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