[Freesurfer] mri_watershed -brain_atlas undocumented?
- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas? Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5 ___ 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.
Re: [Freesurfer] mri_watershed -brain_atlas undocumented?
Hi Tom I'll cc Flo who wrote this code (a long time ago!). I think the -brain_atlas flag takes a gca atlas and uses it to avoid large-scale errors, while -atlas uses some built-in statistics about the shape and size of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me if I'm wrong :) cheers Bruce On Tue, 4 Nov 2014, tvg[fs] wrote: - This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas? Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5 ___ 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 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] mri_watershed -brain_atlas undocumented?
Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas. Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_watershed --version stable5 ___ 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.
