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 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 talairach.lta file. In order to obtain this file, I must run recon-all. However, I do not wish to run recon-all until I have obtained the necessary .gca atlas described above.

Is there possibly some sort of alternative iterative method to create the talairach transform? If so, does it require a different atlas than the MNI305 atlas?

Thanks for the help!

-Mark

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