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. > > > > > > > > > _______________________________________________ > 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
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