--deoblique option will not work in apptainer build

[Jolinda]

What happened?

Running mriqc with the --deoblique option fails because 3drefit from afni is not installed. Perhaps adding 3drefit to the afni packages in the dockerfile under "# Keep only what we use" on line 71 would solve the problem. I have observed this with an apptainer build -- I have not tested with a docker container but it seems likely to have the same issue.

What command did you use?

apptainer run --cleanenv mriqc-24.0.2.simg bidsdir qcdir participant --deoblique --nprocs=16 --no-sub

What version of the software are you running?

24.0.2

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

Work directory

Please copy and paste any relevant log output.

Traceback (most recent call last):
	  File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/afni/base.py", line 124, in _run_interface
	    return super(AFNICommandBase, self)._run_interface(
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
	    raise IOError(
	OSError: No command "3drefit" found on host n0111.talapas.uoregon.edu. Please check that the corresponding package is installed.

Additional information / screenshots

No response