I think 2, but it ignores the GCA if you give it a segmentation.

cheers Bruce On Thu, 18 Jul 2013, Mark Plantz wrote:

Hello freesurfers,     I am currently trying to create a normalized .mgz file using the mri_ca_normalize command. Instead of using a .gca atlas, I am using a manually segmented image.

I have tried using the -seg flag. However, I keep getting an error that I am not inputting the correct arguments. Do you have to include the .gca and transform file in the command, even if they will not be used? The fswiki section on GCA atlases does not seem to touch on this.

For instance, which of the following would be the correct command line?

1.)    mri_ca_normalize -seg <seg_file> <input volume> <output_file>

or

2.) mri_ca_normalize -seg <seg_file> <input volume> <GCA atlas> <transform file> <output_file>

Thanks for the help!

~ Mark