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.eduwrote:

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/datahttp://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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