Hello freesurfers,
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).
My command line is:
mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca
The results:
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 *************************************************************************** processing subject CMH-11460, 1 of 2... reading input 0: /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-11460/mri/T1.mgz *************************************************************************** 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.
Any ideas?
Thanks in advance,
MP