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]$