Hi Tali
can you email me the nu.mgz, the talairach.lta and the brainmask.mgz? I'll
see if I can get it to happen and fix it.
thanks
Bruce
On
Thu, 21 Jul 2011, Tali Swisher wrote:
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
--
Talis M. Swisher, BA
Research Assistant
Psychiatry Neuroimaging Laboratory
Harvard Medical School, Brigham and Women's Hospital
1249 Boylston St, 3rd Floor
Boston, MA 02215
Office: (617) 525-6119
Cell: (336) 577-5071
Fax: (617) 525-6150
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