HCP Pipeline - Nu_correct: Command not found

Software Support
,
1

Summary of what happened:

Hello,

I am trying to run the HCP Pipeline, which uses freesurfer and it is currently failing.

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.

My university installed Freesurfer 6.0 on their High Performance Cluster and I access it via adding a module.

Is anyone able to help?

Command used (and if a helper script was used, a link to the helper script or the command generated):

PASTE CODE HERE

Version:

Environment (Docker, Singularity / Apptainer, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

nu_correct: Command not found.

Screenshots / relevant information:

2

Are you sourcing $FREESURFER_HOME/SetUpFreeSurfer.sh when setting up your shell? That should add the MNI path to your PATH.

1 Like
3

I think I have done this now and $SUBJECTS_DIR gives expected output but not for FSFAST_HOME or MNI_DIR

4

I may have sorted it, the call to FreeSurferEnv.sh had been commented out and I think removing the # will sort me out. If it does I will mark as the solution.

Thank you

1 Like