Hi Guang,
these are some checks we put in to catch common errors in the manual segmentations. In this cause it means we found a Left_Caudate label on the right side of the brain. Did you check any of those voxels to see whether they were wrong? Or maybe your talairach is incorrect? If you specify -check_and_fix it will automatically correct these voxels are write the results into a volume named seg_fixed.mgz
cheers Bruce On Mon, 15 Feb 2010, Guang Zeng wrote:
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
Hotmail: Trusted email with Microsoft?s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/