I recently ran into a problem with mri_ca_train, a function that creates a .gca atlas from a manually segmented volume and input volume(s).
processing subject CMH-11461, 1 of 1...
reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/norm.mgz
filling holes in the GCA...
404261 classifiers: 1.5 per node, 7.59 in brain (0 holes filled)
computing covariances for subject CMH-11461, 1 of 1...
average std = 6.1 using min determinant for regularization = 3.7
298584 singular and 4268 ill-conditioned covariance matrices regularized
writing trained GCA to /Users/IngvalsonLab/Desktop/atlas1.gca...
classifier array training took 0 minutes and 27 seconds.
dhcp-165-124-23-230:LabMRIData IngvalsonLab$
dhcp-165-124-23-230:LabMRIData IngvalsonLab$
dhcp-165-124-23-230:LabMRIData IngvalsonLab$ mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas1.gca
reading T1 data from subject's mri/T1.mgz directory
training on 2 subject and writing results to /Users/IngvalsonLab/Desktop/atlas1.gca
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processing subject CMH-11460, 1 of 2...
reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz
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processing subject CMH-11461, 2 of 2...
reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11461/mri/T1.mgz
filling holes in the GCA...
468392 classifiers: 1.8 per node, 10.41 in brain (0 holes filled)
computing covariances for subject CMH-11460, 1 of 2...
GCAupdateNodeCovariance(17, 35, 28, 4): could not find label
dhcp-165-124-23-230:LabMRIData IngvalsonLab$
According to the fswiki, the same bug was eliminated in the 2009 version. For some odd reason, this command works with one subject, but not with multiple subjects.