check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all.
n. On Wed, 2009-10-07 at 15:34 -0400, Gonzalo Rojas wrote: > Hi: > > I got the following error... How can I solve it ?... > > recon-all.log > ----------------------------------------------------------------- > mri_watershed -T1 -brain_atlas > /usr/local/freesurfer/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=125 y=122 z=99 r=84 > first estimation of the main basin volume: 2562881 voxels > Looking for seedpoints > 2 found in the cerebellum > 16 found in the rest of the brain > global maximum in x=103, y=120, z=70, Imax=255 > CSF=17, WM_intensity=110, WM_VARIANCE=5 > WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 > preflooding height equal to 10 percent > done > Analyze > > main basin size=33359051 voxels, voxel volume =1.000 > = 33359051 mmm3 = 33359.051 cm3 > done > PostAnalyze...Basin Prior > 86 basins merged thanks to atlas > ***** 0 basin(s) merged in 1 iteration(s) > ***** 0 voxel(s) added to the main basin > done > Weighting the input with prior template > > ****************TEMPLATE DEFORMATION**************** > > second estimation of the COG coord: x=127,y=125, z=105, r=9959 > iterations > GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 22212 > RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1368 > LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1242 > RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 9603 > LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=49 , nb = 9792 > OTHER CSF_MIN=0, CSF_intensity=33, CSF_MAX=47 , nb = 207 > mri_watershed Error: > GLOBAL region of the brain empty ! > Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC > 2009 i686 GNU/Linux > > recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
