Hi, there,

I have created our own template and am creating our own atlas now. I have annotation files for each subject in my training set, and my mris_ca_train command line is:

mris_ca_train -n 2 -t /home/freesurfer-install/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot custom_1  custom_2 custom_3 custom_4 lh_myatlas.gcs

my question is here,  I should use the lh.sphere.reg file which register the sphere to the FS default template or the registration file which register the sphere to my own template?

Thanks!
Guang

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