Hi Jason,
those are sanity checks we put in to make sure that we didn't accidentally have say right hippocampal labels in the left hemi. Check the manually labeled subjects and see if they have the wrong hemi label.
cheers, Bruce
On Tue, 11 Nov 2008, Jason S. Minamora wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer