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: fis...@nmr.mgh.harvard.edu
To: andrewz...@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: andrewz...@live.com.au
> To: fis...@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: fis...@nmr.mgh.harvard.edu
> > To: andrewz...@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: fis...@nmr.mgh.harvard.edu
> > > > To: xuelongz...@hotmail.com
> > > > CC: freesurfer@nmr.mgh.harvard.edu; gr...@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: fis...@nmr.mgh.harvard.edu
> > > > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > > > CC: gr...@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.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > _______________________________________________
> > > > > > 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 t
o whom it is
> > > > > > addressed. If you believe this e-mail was sent to you in error a
nd the e-mail
> > > > > > contains patient information, please contact the Partners Compli
ance HelpLine
> at
> > > > > > http://www.partners.org/complianceline . If the e-mail was sent
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> > > > > > but does not contain patient information, please contact the sen
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> > > > > > dispose of the e-mail.
> > > > > >
> > > > >
> > > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
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> > >
> > >
>
>
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