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My group runs an older version of Freesurfer so that when we run recon-all, it creates the 2005 FS atlas. I've installed the current version of FS on a new machine and I'm trying to go back and create DKT atlases for each of our previous patients. I use the following code, hoping to generate an .annot file but get the following output: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh ../surf/lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(../surf/lh.sphere.reg): file magic #fffffe63 != GCSA_MAGIC (ababcdcd) mris_ca_label: could not read classifier from ../surf/lh.sphere.reg if I run it without the file path for the lh.sphere.reg file I get the following: mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs ../label/lh/aparc.DKTatlas.annot GCSAread(lh.sphere.reg): could not open file No such file or directory mris_ca_label: could not read classifier from lh.sphere.reg No such file or directory Thank you for your help!
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