Hi, I'm having a little trouble interpreting the mris_make_average_surface usage and was hpoing for some help:
usage: mris_make_average_surface [options] <hemi> <output surf name> <canon surface> <output subject name> <subject> ... <output subject name > this program will generate an average of the orig surfaces of all the subjects specified (unless the -s <surface name> flag is used) the transform defaults to talairach.xfm in the subject's mri/transforms directory, but can be changed using the -x <xform name> switch
What does the canon surface refer to? Why is there an ouput subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] vertex correspondance they are in correspondence, but there may be shear in the pial deformation, so the link will overestimate the thickness. Easy to compute though, just the distance between the same vertex on the 2 surfaces On Wed, 22 Jun 2005, Fornito, Alexander wrote:
Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance
Hi Alex,
yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that?
Bruce
On Wed, 22 Jun 2005, Fornito, Alexander wrote:
Hi again,
So many questions!!
Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files?
Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this?
Thanks as always,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
alexander.fornito@wh.org.au
Hi Alex,
sorry, the usage is wrong (ignore the <output subject> at the end. It's only the 1st one (the 4th argument) that is used. canon surface is almost always sphere.reg unless you're doing something off the beaten track. You're probably better off using the make_average_surfaces script that Nick wrote, which I've attached. It calls mris_make_average_surfaces a bunch of times and sets up an average subject for your study.
cheers, Bruce
On Mon, 27 Jun 2005, Fornito, Alexander wrote:
Hi, I'm having a little trouble interpreting the mris_make_average_surface usage and was hpoing for some help:
usage: mris_make_average_surface [options] <hemi> <output surf name> <canon surface> <output subject name> <subject> ... <output subject name > this program will generate an average of the orig surfaces of all the subjects specified (unless the -s <surface name> flag is used) the transform defaults to talairach.xfm in the subject's mri/transforms directory, but can be changed using the -x <xform name> switch
What does the canon surface refer to? Why is there an ouput subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] vertex correspondance they are in correspondence, but there may be shear in the pial deformation, so the link will overestimate the thickness. Easy to compute though, just the distance between the same vertex on the 2 surfaces On Wed, 22 Jun 2005, Fornito, Alexander wrote:
Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance
Hi Alex,
yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that?
Bruce
On Wed, 22 Jun 2005, Fornito, Alexander wrote:
Hi again,
So many questions!!
Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files?
Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this?
Thanks as always,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
alexander.fornito@wh.org.au
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fornito, Alexander