mri_ca_train (called from rebuild_gca_atlas.csh) terminated after printing the following to screen:
----------- Log file is /Users/jsm/work/subjects/rebuild_gca_atlas_2008-11-11.log mri_ca_normalize each subject using its seg_edited.mgz, producing norm.mgz... using MR volume /Users/jsm/womri_ca_train using one subject: f18, producing /Users/jsm/work/subjects/average/RB_one_2008-11-11.gca... pbsubmit: Command not found. erate control points... reading 1 input volumes reading atlas from 'noatlas'... reading input volume from /Users/jsm/work/subjects/f18/mri/nu.mgz... bias field = 1.403 +- 0.096 361 of 19551 control points discarded bias field = 0.971 +- 0.051 834 of 34697 control points discarded writing normalized volume to /Users/jsm/work/subjects/f18/mri/norm.mgz... freeing GCA...done. normalization took 2 minutes and 29 seconds. mri_ca_train using one subject: f18, producing /Users/jsm/work/subjects/average/RB_one_2008-11-11.gca... reading input 0: /Users/jsm/work/subjects/f18/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 8.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_man.xfm reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 1 subject and writing results to /Users/jsm/work/subjects/average/RB_one_2008-11-11.gca *************************************************************************** processing subject f18, 1 of 1... reading volume /Users/jsm/work/subjects/f18/mri/brain.mgz for masking... INFO: original RAS-to-RAS transform 1.076 0.007 0.006 -3.332; -0.094 1.129 0.384 -27.287; 0.003 -0.370 1.069 -0.379; 0.000 0.000 0.000 1.000; INFO: modified VOX-to-VOX transform 1.076 0.006 -0.007 -10.648; 0.003 1.069 0.370 -70.266; 0.094 -0.384 1.129 33.189; 0.000 0.000 0.000 1.000; checking labels in subject f18... ERROR: Right_Hippocampus: 104 138 97, tal x=26.245338, y=-27.008644, *** z=14.712428 > 13 *** ERROR: Right_Hippocampus: 104 139 96, tal x=26.232159, y=-28.505787, *** z=14.143823 > 13 *** ERROR: Right_Hippocampus: 104 139 97, tal x=26.239115, y=-27.429529, *** z=13.748710 > 13 *** ERROR: Right_Hippocampus: 105 138 97, tal x=25.179642, y=-26.918175, *** z=14.705179 > 13 *** ERROR: Right_Hippocampus: 105 139 97, tal x=25.173420, y=-27.339060, *** z=13.741462 > 13 *** ERROR: Right_Hippocampus: 106 139 97, tal x=24.107723, y=-27.248587, *** z=13.734215 > 13 *** ERROR: Right_Hippocampus: 110 139 96, tal x=19.837978, y=-27.962954, *** z=14.100336 > 13 *** (...) ERROR: Left_Hippocampus: 155 141 92, tal x=-28.158634, y=-29.038506, *** z=13.427198 > 13 *** ERROR: Left_Hippocampus: 155 141 93, tal x=-28.151674, y=-27.962250, *** z=13.032085 > 13 *** max_xtal_l_hippo = -8.9 max_xtal_l_caudate = -3.3 max_xtal_l_amygdala = -13.1 max_xtal_l_putamen = -11.9 max_xtal_l_pallidum = -10.9 min_xtal_r_hippo = 8.1 min_xtal_r_caudate = 5.2 min_xtal_r_amygdala = 11.4 min_xtal_r_putamen = 11.5 min_xtal_r_pallidum = 12.5 ERROR: mri_ca_train: possible bad training data! subject: /Users/jsm/work/subjects/f18
ERROR: mri_ca_train check found 1 subjects with bad labels!
978 prior holes filled filling holes in the GCA... 38886 classifiers: 1.2 per node, 2.82 in brain (0 holes filled)
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Is there a way to override the default thresholds?
Jason