TypeError: 'Namespace' object does not support item assignment when using --longitudinal or --subject-anatomical-reference unbiased

[joshita89]

Describe the bug
Running sMRIPrep with either --longitudinal or --subject-anatomical-reference unbiased
crashes immediately at startup with:
Traceback (most recent call last):
File "/opt/conda/envs/smriprep/bin/smriprep", line 7, in
sys.exit(main())
File "/opt/conda/envs/smriprep/lib/python3.12/site-packages/smriprep/cli/run.py", line 37, in main
opts['longitudinal'] = True
TypeError: 'Namespace' object does not support item assignment

Also reproduced with --subject-anatomical-reference unbiased instead of --longitudinal — same crash, same line.

Version

Reproduced identically on 0.19.0, 0.19.1, and 0.19.2 (Singularity containers built from docker://nipreps/smriprep).

Exact command line executed
singularity run
--bind $bids_in,$bids_out,$work,$FREESURFER_HOME,$SINGULARITYENV_TEMPLATEFLOW_HOME
/path/to//smriprep-0.19.1.sif
$bids_in $bids_out participant
--participant-label 01
--subject-anatomical-reference unbiased
--fs-license-file $license
--output-spaces MNI152NLin2009cAsym:res-2 fsaverage5
--stop-on-first-crash
-w $work
--skull-strip-template OASIS30ANTs
--nprocs 48 --omp-nthreads 4 --mem-gb 350

Are you positive that the input dataset is BIDS-compliant?

• I have used the online BIDS-Validator
• I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
• [X ] I let sMRIPrep check it for me (in other words, I didn't set the --skip-bids-validation argument).
• No, I haven't checked myself AND used the --skip-bids-validation argument.

sMRIPrep feedback information
Please attach the full log written to the standard output and the crashfile(s), if generated.

Visual reports of sMRIPrep
Traceback (most recent call last):
File "/opt/conda/envs/smriprep/bin/smriprep", line 7, in
sys.exit(main())
^^^^^^
File "/opt/conda/envs/smriprep/lib/python3.12/site-packages/smriprep/cli/run.py", line 37, in main
opts['longitudinal'] = True
~~~~^^^^^^^^^^^^^^^^
TypeError: 'Namespace' object does not support item assignment

Installation type (please complete the following information):

• "Bare-metal"
• [X ] Singularity
• Docker

Additional context
Add any other context about the problem here.