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
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