Error when running FreeSurferPipelineBatch

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Melissa Thalhammer

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Jul 30, 2021, 5:55:19 AM7/30/21
to HCP-Users
Dear all,

I try to run the script "FreeSurferPipelineBatch.sh" which I have adapted from the Examples/Scripts on one subject using Ubuntu 18.04.5 LTS. I keep getting the error return_code 1 (see attached files). Can you provide some help?

Best, Melissa Thalhammer




FreeSurferPipelineBatch.sh
recon-all.log
Screenshot_2021-07-30_11-46-32.png
SetUpHCPPipeline.sh

Glasser, Matthew

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Jul 30, 2021, 7:52:05 AM7/30/21
to hcp-...@humanconnectome.org

It looks like you have both FreeSurfer 5.3 and 6.0 installed and it is finding the MNI tools of 5.3 on your path, which aren’t compatible with Ubuntu 18.04.

 

Matt.

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