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)
-------------
Is there a way to override the default thresholds?
Jason
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