Hello freesurfer gurus.
Recently I was trying to do a fix on a brain that appeared to have a bad
skull strip. The T1 was fine but the brainmask volume came out almost
totally black, with the surfaces confined to some fuzziness in the corner
(appearing very strange in tkmedit). I attempted to fix the skullstrip by
adjusting the watershed, using version 4 to remain consistent with our
other subjects for whom we did recon1 with version 4 to get better
talairachs. Below is the last part of the log. Any ideas?
*********************************************************
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=196 y=119 z=233 r=13
first estimation of the main basin volume: 10195 voxels
mean intensity too low !
Modification of the image: intensity*10.67
first estimation of the COG coord: x=196 y=119 z=233 r=13
first estimation of the main basin volume: 10195 voxels
mri_watershed Error:
Interpolation problem in the white matter curve analysis
Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686
i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Nov 1 16:25:31 CDT 2007
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