template deformation error: global region empty - Freesurfer

16 Jan 2009


      Just wondering if there are any suggestions for finding a work-around when the "global region of the brain empty" error message appears after executing the following command: recon-all -autorecon1 -s CIP_H0519_ERR -notal-check. The T1 image (001.mgz) looks fine. The -notal-check flag was added on the 2nd execution of recon-all due to failure at the talairach_avi stage. Same error occurs in 2/16 subjects we have recently attempted to process using freesurfer v405 on RHEL5.
Many Thanks for any suggestions,
Jenifer
#@# Skull Stripping Fri Jan 16 12:06:43 CST 2009
/usr/local/freesurfer/subjects/CIP_H0519_ERR/mri
mri_watershed -T1 -brain_atlas /usr/local/freesurfer/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=140 y=158 z=147 r=70
      first estimation of the main basin volume: 1469917 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        6 found in the rest of the brain 
      global maximum in x=170, y=133, z=131, Imax=255
      CSF=20, 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=7426225090 voxels, voxel volume =1.000 
                     = 7426225090 mmm3 = 7426225.152 cm3
done
PostAnalyze...Basin Prior
 533 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=172,y=168, z=162, r=9871 iterations
   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 19890
  RIGHT_CER    CSF_MIN=0, CSF_intensity=4, CSF_MAX=10 , nb = 1251
  LEFT_CER     CSF_MIN=0, CSF_intensity=3, CSF_MAX=9 , nb = 1089
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 7686
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 8289
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1575
mri_watershed Error: 
 GLOBAL region of the brain empty !
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Jan 16 12:07:31 CST 2009
[jjuranek@localhost CIP_H0519_ERR]$