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 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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