ANTs Version: 2.5.1.post1-g128c124 still requires ANTSPATH

[postnubilaphoebus]

ANTs Version: 2.5.1.post1-g128c124 still requires ANTSPATH

[gdevenyi]

This is a misconfiguration of your system, not a problem with the removal of ANTSPATH

[cookpa]

It's unusual that $PATH is a single directory. Normally, PATH contains every directory that may be used to execute programs, and you add to PATH for ANTs:

export PATH=/opt/ants/bin:$PATH

This sets PATH to /opt/ants/bin: and whatever PATH was beforehand.

In your case, you would do export PATH=/u/user_name/ants/install/bin:$PATH

[cookpa]

Also, ANTSPATH was only ever required by scripts. Compiled executables like antsRegistration or ImageMath should run once added to the PATH. If this doesn't work, it indicates a problem with the PATH variable.

I'm not that familiar with srun but I assume it runs with whatever $PATH is at run time. If not, there may be an option to set PATH specifically for the command - but again, you'll want to use all the PATH, PATH=/u/user_name/ants/install/bin:$PATH, not just the ANTs bin directory.

[postnubilaphoebus]

@cookpa
I did indeed run a bash script using SLURM instructions on an HPC, and I also specified the PATH as PATH=/u/user_name/ants/install/bin:$PATH. My PATH variable also returned other paths, apologies for the confusion. I will try to reproduce the error and be more specific. Fortunately, the bash script is running with ANTSPATH.

[dorianps]

srun $PATH/antsRegistration: maybe you need to remove $PATH from that. You are prepending the entire PATH list to the call for antsRegistration? Also, you can try running "which antsRegistration" to see where does the system think antsRegistration should be.

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On Fri, Jan 26, 2024 at 10:19 AM Laurids Stockert ***@***.***> wrote: @cookpa <https://github.com/cookpa> I did indeed run a bash script using SLURM instructions on an HPC, and I also specified the PATH as PATH=/u/user_name/ants/install/bin:$PATH. My PATH variable also returned other paths, apologies for the confusion. I will try to reproduce the error and be more specific. Fortunately, the bash script is running with ANTSPATH. — Reply to this email directly, view it on GitHub <#1667 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFJU7KCB4KSWLJVP26KONDYQPCQTAVCNFSM6AAAAABCMGKN76VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJSGIZTOMZSGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>