Hello again,
I've been having some problems with FS segmentation, especially around the temporal lobes, where there is a clear underestimation of the pial surface (and manual edits are not being too successful). The problem is clearly related to the poor resolution of the used images.
Are there any parameters to change in order to optimise the segmentation process?
Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else?
Thank you again.
Joao Pereira
what is the resolution of your images? You might as well send us the complete set of acquisition parameters. Bruce
On Tue, 6 Jun 2006, Joao Pereira wrote:
Hello again,
I've been having some problems with FS segmentation, especially around the temporal lobes, where there is a clear underestimation of the pial surface (and manual edits are not being too successful). The problem is clearly related to the poor resolution of the used images.
Are there any parameters to change in order to optimise the segmentation process?
Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else?
Thank you again.
Joao Pereira
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I have just realized I made a mistake when I ran recon-all -s subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is overridden by autorecon1. Nevertheless, when I look at the dates of the files, I see that talairach.xfm is the one I edited, although talairach.log has a posterior date. Moreover, when I look at the transforms with tkregister2, they seem just as I have left them. What am I missing here?
Thanks!
Joao
Hi Joao,
Sorry for the late response, but I've been away for two weeks ...
When recon-all is first run (and there is not talairach.xfm), it will create talairach.auto.xfm and copy that to talairach.xfm. In subsequent runs, recon-all will create a new talairach.auto.xfm. Immediately prior to this, it will check to see whether talairach.auto.xfm is the same as talairach.xfm. If they are the same, it assumes that you have not made any manual edits to it and it will copy the newly generated talariach.auto.xfm to talairach.xfm. If there are differences, it generates the new talairach.auto.xfm but does not copy it. This is overridden when you add -clean-talairach. It is done this way to help protect the user from accidentally overwriting manual changes. This strategy is also used with brainmask.mgz.
doug
Joao Pereira wrote:
Hi,
I have just realized I made a mistake when I ran recon-all -s subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is overridden by autorecon1. Nevertheless, when I look at the dates of the files, I see that talairach.xfm is the one I edited, although talairach.log has a posterior date. Moreover, when I look at the transforms with tkregister2, they seem just as I have left them. What am I missing here?
Thanks!
Joao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Joao Pereira