[Freesurfer] talairach and MNI305 Atlas

2013-07-15 Thread Mark Plantz
Hello freesurfers, I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for infant MRI's. Currently, I have three of the four required arguments. I am lacking the

Re: [Freesurfer] talairach and MNI305 Atlas

2013-07-15 Thread Bruce Fischl
Hi Mark do you have a segmentaton for the brain? Bruce On Mon, 15 Jul 2013, Mark Plantz wrote: Hello freesurfers,     I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for

Re: [Freesurfer] talairach and MNI305 Atlas

2013-07-15 Thread Douglas N Greve
Mark, you can run recon-all -s subject -motioncor -talairach And it will run it upto the creation of the talairach matrix. If you only have one run, then you don't need -motioncor doug On 07/15/2013 12:35 PM, Mark Plantz wrote: Hello freesurfers, I am currently attempting to create