You are missing a switch before the ../label/lh.cortex.label parameter (-l I think? Read the help). That makes all the positional parameters apparently in the wrong place

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rollo, Patrick
Sent: Tuesday, October 20, 2020 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error running mris_ca_label

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Experts,

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!