Hi FS experts,
I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance.
Liang
Hi Liang,
you should just be able to use the -rl (reslice like) option in mri_convert and give the orig/001.mgz as the target.
cheers Bruce
On Fri, 12 Mar 2010, liang wang wrote:
Hi FS experts,
I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance.
Liang
Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison
Hi Allison and Bruce,
Thanks for your kind explanations and the website mentioned http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I am curious why I can not directly find this website from the main interface http://surfer.nmr.mgh.harvard.edu/fswiki. Is there a website listing all the great links. Thanks.
Liang
2010/3/15 Allison Stevens astevens@nmr.mgh.harvard.edu
Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison
--
On Sat, 13 Mar 2010, Bruce Fischl wrote:
Hi Liang,
you should just be able to use the -rl (reslice like) option in mri_convert and give the orig/001.mgz as the target.
cheers Bruce
On Fri, 12 Mar 2010, liang wang wrote:
Hi FS experts,
I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance.
Liang
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.
Hi Liang,
are you doing a "text" search on the wiki? Hopefully that would find it. The "titles" search is useless.
cheers, Bruce On Tue, 16 Mar 2010, liang wang wrote:
Hi Allison and Bruce,
Thanks for your kind explanations and the website mentioned http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I am curious why I can not directly find this website from the main interface http://surfer.nmr.mgh.harvard.edu/fswiki. Is there a website listing all the great links. Thanks.
Liang
2010/3/15 Allison Stevens astevens@nmr.mgh.harvard.edu
Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison
--
On Sat, 13 Mar 2010, Bruce Fischl wrote:
Hi Liang,
you should just be able to use the -rl (reslice like) option in mri_convert and give the orig/001.mgz as the target.
cheers Bruce
On Fri, 12 Mar 2010, liang wang wrote:
Hi FS experts,
I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance.
Liang
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.
I've also been trying to link these type of pages on here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Bruce Fischl -
liang wang