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
