New container mrtrix3 3.0.4

[vnm-neurodesk]

There is a new container by @stebo85, use this command to test:

bash /neurocommand/local/fetch_and_run.sh mrtrix3 3.0.4 20240316

If test was successful, then add to apps.json to release:
https://github.com/NeuroDesk/neurocommand/edit/main/neurodesk/apps.json

Please close this issue when completed :)

[stebo85]

@joelleinkauf - can you test if this container works?

[joelleinkauf]

Works well now, thank you so much!

[stebo85]

Great :) The new verison is now released and is available through the Application menu after clicking on update:

and it's available through the module system:

Thank you for finding this problem and proposing a solution!

[joelleinkauf]

Sorry to bother again, but it seems as though the issue is not yet resolved. After module load I tried the command but it again did not find the liblapack3 and showed me again: " ACPCdetect not installed". Do you have any idea why this could be?

[stebo85]

Can you post here, which commands exactly you are running? Could it be that you installed ACPCdetect outside of the mrtrix container separately?

[stebo85]

OK, so I think I know what's going on: You have acpcdetect installed outside of the mrtrix container and when calling 5ttgen through the module system you cannot see this binary:

acpcdetect needs to be installed inside the mrtrix container. I will try that now.

[stebo85]

Ok, can you try again? Before you try your script, can you check that acpcdetect is found and is pointing to /cvmfs/neurodesk.ardc.edu.au/containers/mrtrix3_3.0.4_20240319/acpcdetect

(base) jovyan@neurodesktop-:~$ ml mrtrix3
(base) jovyan@neurodesktop-:~$ ml

Currently Loaded Modules:
  1) mrtrix3/3.0.4

(base) jovyan@neurodesktop-:~$ which acpcdetect 
/cvmfs/neurodesk.ardc.edu.au/containers/mrtrix3_3.0.4_20240319/acpcdetect
(base) jovyan@neurodesktop-:~$ 

[joelleinkauf]

Thank you for your time, and indeed I was wondering that too! Now I tried it like you told me to: "ml mrtrix3/3.0.4" , "which acpcdetect" - and it was pointing to the container path- "/cvmfs/neurodesk.ardc.edu.au/containers/mrtrix3_3.0.4_20240319/acpcdetect", then I tried running 5ttgen normally "5ttgen ..." and I got the same error again: "ACPCdetect not installed".

[stebo85]

When I run 5ttgen after that module load I am not getting this error. Can you send me a minimal example that produces this error?

[joelleinkauf]

Here is the snippet:
(base) jovyan@neurodesktop-:$ ml mrtrix3/3.0.4
(base) jovyan@neurodesktop-:$ which acpcdetect
/cvmfs/neurodesk.ardc.edu.au/containers/mrtrix3_3.0.4_20240319/acpcdetect
(base) jovyan@neurodesktop-:~$ 5ttgen hsvs /home/jovyan/freesurfer-subjects-dir/sub-02_connectome_recon/ 5ttTry.mif
5ttgen:
5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
5ttgen:
5ttgen: Generated scratch directory: /home/jovyan/5ttgen-tmp-TNG5C7/
Command: mrconvert /home/jovyan/freesurfer-subjects-dir/sub-02_connectome_recon/mri/aparc+aseg.mgz /home/jovyan/5ttgen-tmp-TNG5C7/aparc.mif
5ttgen: Changing to scratch directory (/home/jovyan/5ttgen-tmp-TNG5C7/)
Command: mrconvert /home/jovyan/freesurfer-subjects-dir/sub-02_connectome_recon/mri/norm.mgz T1.nii -stride -1,+2,+3
5ttgen: [WARNING] ACPCdetect not installed; cannot segment anterior commissure

[stebo85]

Ok, I think I found the problem. 5ttgen doesn't actually check if acpcdetect is installed, it looks for an environmentvariable called ARTHOME

so setting this:

export SINGULARITYENV_ARTHOME=/opt/acpcdetect_V2.1/

before running 5ttgen works

Can you quickly test and then I will build that into the image

[joelleinkauf]

Great, tried it with module load and "export SINGULARITYENV_ARTHOME=/opt/acpcdetect_V2.1/" and it works well now!

[stebo85]

Great :) Thank you for confirming. It's released now and incorporated in the mrtrix3_3.0.4_20240320 container and you don't need the export SINGULARITYENV_ARTHOME=/opt/acpcdetect_V2.1/ anymore :)