hi bruce,

mri_watershed failed.

cheers,

satra


 mri_watershed -T1 -brain_atlas /nitrc/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
Weighting the input with atlas information before watershed

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=127 y=129 z=144 r=65
      first estimation of the main basin volume: 1176865 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=102, y=106, z=114, Imax=255
      CSF=12, 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=19240706014 voxels, voxel volume =1.000 
                     = 19240706014 mmm3 = 19240706.048 cm3
done.
PostAnalyze...Basin Prior
 0 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=128,y=136, z=125, r=9654 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

mri_watershed Error: 
 GLOBAL region of the brain empty !


On Fri, Jul 5, 2013 at 10:03 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Satra

what was the error? Pretty poor gray/white contrast in the data.

cheers
Bruce


On Fri, 5 Jul 2013, Satrajit Ghosh wrote:

hi bruce and others:

i'm getting a recon failure on this particular brain: H0351.1009

the quality isn't great, but if you can take a quick look at the brain to
see if you can spot any particular issues, that would be great.

4 of the others finished recon and 3 are almost there.

cheers,

satra

data location: http://human.brain-map.org/mri_viewers/data

command:  recon-all -subjid H0351.1009 -all -i
/data/allen/H0351.1009/T1.nii.gz -openmp 8 -notalairach

==> /data/subjects/H0351.1009/scripts/recon-all-status.log <==
status file for recon-all
Fri Jul  5 00:02:39 UTC 2013
#@# MotionCor Fri Jul  5 00:02:43 UTC 2013
#@# Nu Intensity Correction Fri Jul  5 00:02:57 UTC 2013
#@# Intensity Normalization Fri Jul  5 00:04:45 UTC 2013
#@# Skull Stripping Fri Jul  5 00:07:53 UTC 2013
Linux node007 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s H0351.1009 exited with ERRORS at Fri Jul  5 00:16:26 UTC 2013





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