Looks like the skull stripping failed. Can you visually inspect the talairach xform? Why did you turn checking off?

On May 23, 2013, at 6:26 PM, stdp82@virgilio.it wrote:

Hi list,

I'm performing

recon-all -all -notal-check -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR -cw256

on a T1 with following info: data_type INT16 dim1 280 dim2 240 dim3 240 dim4 1 datatype 4 pixdim1 0.5999908447 pixdim2 1.0416666269 pixdim3 1.0416666269 pixdim4 0.0000000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+

and I have this error

(2) Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=55 , nb = 36036 RIGHT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 3042 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 3852 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=179 , nb = 14652 LEFT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=99 , nb = 14058 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 432 mri_watershed Error: GLOBAL region of the brain empty ! Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64

recon-all -s SUBJECTS_DIR exited with ERRORS at Fri May 24 00:04:27 CEST 2013

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Complete .log file is also attached.

What's happen?

Thanks,

Stefano <recon-all.log> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer