Hello,
We are having some trouble with autorecon1, specifially the watershed step. Here's the error we get:
#-------------------------------------------- #@# 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