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 sphere. > Should I > be using some other flags? For instance, if I used -w 1 instead, would this > 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 it > 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 > > > 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: 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 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: fis...@nmr.mgh.harvard.edu > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > CC: gr...@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 > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > > whom it is > > > > > > addressed. If you believe this e-mail was sent to you in error and > > > > > > the e-mail > > > > > > contains patient information, please contact the Partners > > > > > > Compliance HelpLine > at > > > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > > > > you in > error > > > > > > but does not contain patient information, please contact the sender > > > > > > and > properly > > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ 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 to whom it is addressed. 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