Hi all,
I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through mri_ca_normalize (error message below) - any ideas??
Thanks! Tali Swisher
#@# CA Normalize Thu Jul 21 12:25:47 EDT 2011 /home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 using (122, 88, 141) as brain centroid... mean wm in atlas = 107, using box (106,72,120) --> (137, 104,162) to find MRI wm before smoothing, mri peak at 215 after smoothing, mri peak at 214, scaling input intensities by 0.500 scaling channel 0 by 0.5 using 244171 sample points... INFO: compute sample coordinates transform 1.134 0.005 0.006 -38.602; 0.006 1.132 0.138 -19.653; 0.004 -0.150 1.048 -20.038; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (142, 46, 61) --> (202, 147, 218) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 111.0 19 of 76 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (87, 48, 60) --> (144, 148, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 107.0 27 of 73 (37.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (146, 122, 85) --> (188, 161, 136) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 105.0 5 of 18 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (103, 122, 83) --> (144, 160, 137) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 108.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (130, 115, 118) --> (158, 176, 147) Segmentation fault Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011