Nibabies: missing 1 required positional argument: 'subjects_dir'

Software Support
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1

Summary of what happened:

I’m trying to run nibabies on my dataset, but it gives me the following error: missing 1 required positional argument: 'subjects_dir'

Command used (and if a helper script was used, a link to the helper script or the command generated):

SINGULARITY_TMPDIR=$PWD 
SINGULARITY_CACHEDIR=$PWD 
singularity run --cleanenv \
-B /EBC/local/infantFS/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
-B /EBC/home/mblesa/nibabies_test/BIDs:/data:ro \
-B /EBC/home/mblesa/nibabies_test/results:/out \
../nibabies-24.0.0a1.sif \
/data /out participant \
--age-months 0 \
--anat-only \
--fs-no-reconall \
--nprocs 16 --omp-nthreads 16 \
--participant-label 8018 --session-id 01 \
--output-spaces anat MNIInfant:cohort-2:res-native -vvv

Version:

24.0.0 - alpha 1

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

         Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.11.0
(node:23142) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
        1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

        Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.

        2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)

        Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.

        Summary:                 Available Tasks:        Available Modalities:
        12 Files, 57.25MB                                MRI
        1 - Subject
        1 - Session


        If you have any questions, please post on https://neurostars.org/tags/bids.
240430-09:22:15,896 nipype.workflow IMPORTANT:

    Running nibabies version 24.1.0.dev35+g7b1e91d:
      * BIDS dataset path: /data.
      * Participant list: [['8018', '01']].
      * Run identifier: 20240430-092159_d78de70a-4b08-4c16-9353-18632c84c704.
      * Output spaces: anat MNIInfant:cohort-2:res-native.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.

Relevant log outputs (up to 20 lines):

nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gen_recon_outdir.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
          File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
            out = function_handle(**args)
        TypeError: _gen_recon_dir() missing 1 required positional argument: 'subjects_dir'

Screenshots / relevant information: