Hello,
While doing a autorecon-all, I experienced an error during the template
deformation step.
writing output transformation to transforms/talairach_with_skull.lta...
registration took 187 minutes and 39 seconds.
mri_watershed -T1 -brain_atlas
/usr/local/freesurfer/stable4/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for
details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=128 y=93 z=111 r=96
first estimation of the main basin volume: 3776534 voxels
Looking for seedpoints
2 found in the cerebellum
10 found in the rest of the brain
global maximum in x=146, y=87, z=88, Imax=255
CSF=15, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done
Analyze
main basin size=1213505248 voxels, voxel volume =1.000
= 1213505248 mmm3 = 1213505.248 cm3
done
PostAnalyze...Basin Prior
0 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=125,y=102, z=116, r=8049
iterations
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 7803
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 378
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 504
RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1809
LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1152
OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 882
mri_watershed Error:
GLOBAL region of the brain empty !
Linux seymour 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:20:55 EDT 2009 i686
i686 i386 GNU/Linux
Here is my info.
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311
RedHat release: CentOS release 5.3 (Final)
Kernel info: Linux 2.6.18-128.7.1.el5 i686
NMR Center info (/space/freesurfer exists):
machine: seymour
SUBJECTS_DIR: /space/seymour/1/users/MTH_Study/
PWD: /space/newdata/1/siemens
ssh seymour
setenv SUBJECTS_DIR /space/seymour/1/users/MTH_Study/
cd /space/newdata/1/siemens
---------------------------------------------------------------------
Please include the following additional information in your report:
1) subject name
2) the entire command-line executed
3) the error message generated
4) optionally include the subject's /script/recon-all.log
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Please write when you can, and thanks,
Dave
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