Hi, there,

I am using the rebuild_gca_atlas.csh to build our own subcortical atals now, and met a problem at the second step which is

# Train using ONE_SUBJECT, the command line is:

mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_man.xfm -T1 norm.mgz -check $OneID /data1/radiology/m047599/temp_fs_2/freesurfer-v4.5.0/subjects/average/RB_12-Feb-2010.gca

and it gave me errors such as;

ERROR: Left_Caudate: 104 167 182, tal *** x=22.896236 > 5 ***, y=33.105412, z=-16.869007
ERROR: Left_Caudate: 104 167 183, tal *** x=22.900818 > 5 ***, y=34.053909, z=-16.893997
ERROR: Left_Caudate: 104 167 184, tal *** x=22.905401 > 5 ***, y=35.002407, z=-16.918985
ERROR: Left_Caudate: 104 167 185, tal *** x=22.909985 > 5 ***, y=35.950901, z=-16.943975
ERROR: Left_Caudate: 104 167 186, tal *** x=22.914564 > 5 ***, y=36.899403, z=-16.968966
ERROR: Left_Caudate: 104 167 187, tal *** x=22.919147 > 5 ***, y=37.847897, z=-16.993954
ERROR: Left_Caudate: 104 167 188, tal *** x=22.923729 > 5 ***, y=38.796391, z=-17.018944

Why it will have an error related to Left_Caudate? Is the FreeSurferColorLut.txt file called somewhere ?

Thanks!
Guang

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