Try running this:
recon-all -skullstrip -no-wsgcaatlas -s <subjid>
If that goes through without error, you can finish processing your data by
running:
recon-all -autorecon2 -autorecon3 -s <subjid>
Allison
--
On Wed, 17 Mar 2010, Gabriel Go.Es. wrote:
I was trying to run a recon-all and I recibe an error message, wich you can
find attached (recon-all.log),
it appears to be a rpoblem with the skull stripping (the watershed) i tryed the
flag -nowatershed, but the recon does not work. what can i do???
any help will be so apreciated
Best Regards
Gabriel
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=127,y=105, z=104, r=9864 iterations
GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 22419
RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=51 , nb = 1530
LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1332
RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 9837
LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 9522
OTHER CSF_MIN=2, CSF_intensity=16, CSF_MAX=47 , nb = 198
mri_watershed Error:
GLOBAL region of the brain empty !
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006
x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Mar 15 09:45:02 CET 2010
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