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)
*
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
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