FreeSurferPipelineBatch.sh - nu_correct: Command not found.

[Scott Gurney]

Hello,

I am following the Running the HCP Pipelines on example data on GitHub and have ran into an issue when running the FreeSurferPipelineBatch.sh script.

The PreFreeSurferPipelineBatch.sh appears to have ran fine and did not produce any errors.
I believe I have install all the required prerequisite and modified the required variables correctly.

I have attached my log files and you appreciate your assistance.

Thank you in advance, Scott

 

[Glasser, Matt]

That suggests there is something wrong with either your FreeSurfer install or having FreeSurfer binaries accessible on the PATH.

 

Matt.

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[Scott Gurney]

Hi Matt

Thank you for your reply.

Is there a way to test the nu_connect function outside of the hcp_pipeline?

My university installed Freesurfer 6.0 on their High Performance Cluster, so I'd assume it is correct and I access it via adding a module.

I am able to use `echo $FREESURFER_HOME` and get an expected output
If I navigate to that location I can find nu_connect within FREESURFER_HOME/mni/bin but not within FREESURFER_HOME/bin

Sorry for the additional request for assistance, any help to further investigate would be greatly appreciated

[Tim Coalson]

Sourcing the freesurfer setup script should add mni/bin to the path also (and fsfast/bin and tktools).  It sounds like your environment doesn't actually source it (or sets NO_MINC or other modifiers first), and what it did add to PATH didn't include mni/bin.

Tim

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[Scott Gurney]

Thank you, Tim

It was an issue with SetUpFreeSurfer.sh having the final line commented out preventing FreeSurferEnv.sh from being called and setup. Uncommenting this line and sourcing the SetUpFreeSurfer.sh file allowed the 2nd stage to run.

The 2nd stage appears to have completed correctly, but I have 4x the following 'errors' within the FreeSurferPipeline.sh.e file
/gpfs/software/ada/freesurfer/6.0/tktools/tkregister2.bin: /gpfs/software/ada/python/anaconda/2020.11/3.8/lib/libuuid.so.1: no version information available (required by /lib64/libSM.so.6)
Is this anything to be concerned about?

Thank you again, Scott