Re: [Freesurfer] How to transform brain.mgz back to native space

2010-03-16 Thread liang wang
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

Re: [Freesurfer] How to transform brain.mgz back to native space

2010-03-16 Thread Bruce Fischl
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

Re: [Freesurfer] How to transform brain.mgz back to native space

2010-03-16 Thread Allison Stevens
I've also been trying to link these type of pages on here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ -- On Tue, 16 Mar 2010, Bruce Fischl wrote: Hi Liang, are you doing a text search on the wiki? Hopefully that would find it. The titles search is useless. cheers,

Re: [Freesurfer] How to transform brain.mgz back to native space

2010-03-15 Thread Allison Stevens
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:

Re: [Freesurfer] How to transform brain.mgz back to native space

2010-03-13 Thread Bruce Fischl
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

[Freesurfer] How to transform brain.mgz back to native space

2010-03-12 Thread liang wang
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