access to pyAIMS on new singularity distribution

[sarafv]

Hello,

I moved to BrainVISA 5.0.4 that I installed with Singularity. How can I access to BrainVISA's python to run a python script involving AIMS?

Thank you

Sara

[denisri]

Hi,
Once you have setup an environment as explained in the install instructions, and set the bin/ directory into your host system PATH, you can either open a bash shell in the container (bv bash) and run python scripts from it, or run them using bv python script.py. The entry point to the container is the bv command, which runs singularity with the needed options.
Denis

[sarafv]

thank you!, this is working for me . Here an example of my command :

Extracting sulci meshes :

/home/sara.fernandezvidal/epi_projects/epiSTIM_project/software/brainvisa/bin/bv python /home/sara.fernandezvidal/epi_projects/epiSTIM_project/epiSTIM/share/aims_scripts/aims_merge_sulci_mesh.py /home/sara.fernandezvidal/epiloc/brainvisa_databases/newdb/brainvisa_db/patients/CHAm/t1mri/default_acquisition/default_analysis/folds/3.1/LCHAm.arg /tmp/tmpp5wv9l2e/sulci.ply

And after converting ply on vtk :