Hi Matthieu

typically this means something is wrong witheither the input image (T1.mgz) or the talairach_with_skull.lta transform. You can try running it without the atlas and see if that fixes it.

cheers Bruce

On Thu, 16 Mar 2017, Matthieu Vanhoutte wrote:

Dear Freesurfer's experts, I ran a classic recon-all and got stucked on a problem I couldn't find in the mailing list: "mri_watershed Error: indices out of bounds"

mri_watershed -T1 -brain_atlas /home/global//freesurfer5.3//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)

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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=125 y=200 z=49 r=52       first estimation of the main basin volume: 593173 voxels mri_watershed Error: indices out of bounds

Linux woody 4.4.0-31-generic #50~14.04.1-Ubuntu SMP Wed Jul 13 01:07:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 207078_M1_2013-01-29 exited with ERRORS at Thu Mar 16 14:57:24 CET 2017

Do you have idea or clue to this problem ?

Best regards, Matthieu