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.
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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
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
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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Xuelong Zhao