> Hello, > > We are having some trouble with autorecon1, specifially the watershed step. > Here's the error we get: > > > > #-------------------------------------------- > > [EMAIL PROTECTED] Skull Stripping Tue Nov 18 15:19:59 EST 2008 > > /autofs/space/madrc_007/users/adeluca/RETRRO_structural/RETRRO_20_old/mri > > > > 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=108 z=113 r=76 > > first estimation of the main basin volume: 1871279 voxels > > > > > > > > ******************************************* > > *********************************************** > > *********************************************** > > White matter intensity 0 is lower than CSF intensity 18. > > Please examine input images. Will terminate ... > > *********************************************** > > *********************************************** > > *********************************************** > > > > ********************************************************** > > MRIstripSkull failed. > > ************************************************************ > > Linux aubz 2.6.18-92.1.10.el5 #1 SMP Tue Aug 5 07:42:41 EDT 2008 x86_64 > > x86_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Tue Nov 18 15:20:09 EST 2008 > > > Looking at the input file (nu.mgz) it is obvious that the qcquired image isn't > as good as it could be. Looks like there is moderate white matter burden, > dropout on the ventral side of the scan, and some artifacts possibly made > because of dental implants. > > Are there any other steps that can be taken besides marking control points and > adding the -f flag to mri_normalize? > > Thanks, > Jon > >
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