try running it with -no-wsgcaatlas On Thu, 22 Apr 2010, Dave Brohawn wrote:
> 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 > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
