Apptainer Qt library problems

[Drew Parker]

Hello,

I have pulled dsi_studio latest sif image from docker with: 

apptainer pull docker://dsistudio/dsistudio:latest

and running into a wall with every way I try to run dsi_studio --version 

/opt/dsi-studio/dsi_studio: error while loading shared libraries: libQt6Core.so.6: cannot open shared object file: No such file or directory

I have seen that qt exists within the container, inside /opt/qt6/6.5.0/gcc_64/lib 

However, nothing I try can get around the library error. I have run with LD_LIBRARY_PATH explicitly set by apptainer to this internal path, and other combinations 

How can I use this container?  I am running apptainer version 1.3.2-1.el7 on centos7 

All I want to do is convert .sz files from CoRR data repository into nifti bval/bvec files. Is there another tool that can do this conversion? 

Thanks,

Drew Parker 

[Frank Yeh]

Hi Drew,

The libQt6Core.so.6 error you are seeing is a common issue when
running newer Qt6-based containers on CentOS 7. CentOS 7 uses an older
Linux kernel (3.10), and Qt6 relies on newer system calls that aren't
available on that kernel. This causes the library to fail to load,
even if it is physically present inside the container. Apptainer can
also sometimes strip out the LD_LIBRARY_PATH environment variable set
by Docker. You could try explicitly passing it by prefixing your
command with APPTAINERENV_LD_LIBRARY_PATH="/opt/qt6/6.5.0/gcc_64/lib",
but the OS kernel mismatch will likely still be a roadblock.

Since your main goal is simply to convert the CoRR .sz files to NIfTI,
you actually don't need to fight with the container. The .sz format is
essentially a gzip-compressed MATLAB v4 file, which means it can be
unzipped and processed directly with a few lines of Python.

We have a ready-to-use Python script in the DSI Studio documentation
specifically designed to convert .sz files into 4D NIfTI, bval, and
bvec files using scipy.io and nibabel. You can find the full code
snippet under Example 3 on this page:

https://dsi-studio.labsolver.org/doc/cli_data.html

If you do end up running DSI Studio on a system with a newer OS (or if
you pull an older, Qt5-based DSI Studio image), the built-in command
to natively run this conversion is:

dsi_studio --action=rec --source=your_data.sz --save_nii=your_data_dwi.nii.gz

Hope this helps you bypass the Apptainer headaches and get your data
converted smoothly. Let me know if you run into any other problems!

Warmly,

Frank