have you looked at the T1.mgz? Is it ok? Does the talairach.xfm look
reasonable?
On Fri, 21 Nov 2008, Dashkoff, Jonathan David wrote:
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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