Using executables from multiple containers

[npavlovikj]

Dear,

I have a question regarding using executables from multiple containers.

For example, I want to use the executable @SUMA_Make_Spec_FS from afni, that uses mris_convert from freesurfer underneath.
Based on this, https://neurostars.org/t/mris-convert-within-fmriprep-docker/23026/5, my understanding was that I can load multiple modules/containers and the executables from both should be available to each other.

However, that is not the case in my test:

(neurocommand) [npavlovikj@~ neurocommand]$ module load freesurfer/7.3.2
(neurocommand) [npavlovikj@~ neurocommand]$ module load afni/21.2.00 
(neurocommand) [npavlovikj@~ neurocommand]$ @SUMA_Make_Spec_FS -sid SK11 -fspath /work/npavlovikj/data_test/
++ Running @SUMA_Make_Spec_FS version: 2.2.4
program not found in path: mris_convert
1 program(s) not found
program failure: exiting...

mris_convert is part of the freesurfer module, and both loaded modules are part of my $PATH variable:

(neurocommand) [npavlovikj@~ neurocommand]$ which mris_convert
/lustre/work/npavlovikj/neurocommand/local/containers/freesurfer_7.3.2_20220812/mris_convert

(neurocommand) [npavlovikj@~ neurocommand]$ echo $PATH
/work/npavlovikj/neurocommand/local/containers/afni_21.2.00_20210714:/work/npavlovikj/neurocommand/local/containers/freesurfer_7.3.2_20220812:/home/npavlovikj/.conda/envs/neurocommand/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/util/opt/bin

Am I missing something in my setup to have this working?
I just cloned the neurocommand repo, so I am using the newest version available on master.

In the discussion here, https://github.com/orgs/NeuroDesk/discussions/210, the mris_convert executable from freesurfer was added to a newer version of the afni container.
However, my understanding of NeuroDesk is that this can also be achieved by loading the individual afni and freesurfer modules?
Is this not necessarily true?

I would appreciate any feedback or suggestion you can provide.

Thank you!

--
Natasha

[stebo85]

Dear @npavlovikj

Excellent question :)

The reason that mris_convert cannot be found in your example is the following:

Once you execute @SUMA_Make_Spec_FS

then this is running inside the afni container and this script can only see things that are on the path inside the afni container. You are using
the afni/21.2.00 container, which didn't have mris_convert included yet. If you switch to a later afni container version (e.g. 23.0.07) mris_convert is included and on the path inside the afni container, so your error will disappear :)

The module loading of executables will only work if binaries are not nested, e.g. you can call @SUMA_Make_Spec_FS and it will run inside afni and you can call mris_convert and it will run inside the freesurfer container. But the afni container (and therefore @SUMA_Make_Spec_FS) cannot talk to the freesurfer container - otherwise we would end up in an unreproducible setup.

Let us know if this works for you and makes sense :)

[npavlovikj]

Dear Steffen,

Thank you so much for the prompt reply and nice clarification - that all makes sense to me now.

Thank you,
Natasha