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Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the input to watershed.

Thanks, Boris

Am 11.10.2018 um 18:55 schrieb Bruce Fischl fischl@nmr.mgh.harvard.edu:

Hi Boris

can you check to make sure that the input to the watershed looks ok? Also, in general it is a lot easier for us to help if you send us the full command line and screeen output and attach the recon-all.log

cheers Bruce

On Thu, 11 Oct 2018, Boris Rauchmann wrote:

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When I run recon-all i get the follwing error message: mri_watershed Error: GLOBAL region of the brain empty ! Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018 The .nii file looks fine. Can someone help me with this? Best, Boris

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It would be great if you can have a look at the nu.mgz and talairach.xmf but unfortunately I´m not able to provide it in the mailing list. Is there another way to send you the files?

Thanks, Boris

Am 11.10.2018 um 22:04 schrieb Bruce Fischl fischl@nmr.mgh.harvard.edu:

Hi Boris

the input to that watershed call is the T1.mgz, but it is already problematic as you can see from the log. You should take a look at the nu.mgz and make sure it is correct. You can also email me the nu.mgz and the talairach.xfm (in the mri/transforms dir) if you want and I'll take a look cheers Bruce

On Thu, 11 Oct 2018, Boris Rauchmann wrote:

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Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the input to watershed.

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