Summary of what happened:
Hello,
I am running the nibabies pipeline using singularity. My data passes the BIDS check, but I am getting an error: Local Variable 'raw sources' referenced before assignment. I am running nibabies after running BIBSnet to get the derivatives path.
Also, I don’t know what the None refers to in the participant list that is output after I submit the command.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv -B $path/BIBSnet_inputs:/data:ro -B $path/BIBSnet_outputs_nibabies:/out -B /usr/local/freesurfer/6.0.0/license.txt:/opt/freesurfer/license.txt:ro $path/scripts/Kelly/infant/nibabies/nibabies-23.1.0.sif /data /out participant --derivatives $path/BIBSnet_outputs/bibsnet/ --anat-only
Version:
23.1.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator@1.11.0
1: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. 'Slice Timing' is the time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. (code: 13 - SLICE_TIMING_NOT_DEFINED)
./sub-007/ses-02/func/sub-007_ses-02_task-langloc_bold.nii.gz
Please visit https://neurostars.org/search?q=SLICE_TIMING_NOT_DEFINED for existing conversations about this issue.
2: [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.
3: [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:
41 Files, 383.27MB MRI
11 - Subjects
2 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
(node:1295) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
Relevant log outputs (up to 20 lines):
INFO: underlay of /etc/localtime required more than 50 (109) bind mounts
240122-16:07:10,345 nipype.workflow IMPORTANT:
Running nibabies version 23.1.0:
* BIDS dataset path: /data.
* Participant list: **[['007', None]**, ['008', None], ['009', None], ['010', None], ['012', None], ['015', None], ['016', None], ['017', None], ['018', None], ['019', None], ['053', None]].
* Run identifier: 20240122-160654_5ef980ae-9020-4cff-9c17-f299d895183f.
* Output spaces: MNIInfant.
* Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module>
sys.exit(main())
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/cli/run.py", line 63, in main
retval = build_workflow(config_file)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/cli/workflow.py", line 80, in build_workflow
retval["workflow"] = init_nibabies_wf(config.execution.unique_labels)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/workflows/base.py", line 130, in init_nibabies_wf
single_subject_wf = init_single_subject_wf(
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/workflows/base.py", line 371, in init_single_subject_wf
else init_infant_single_anat_wf(**wf_args)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/workflows/anatomical/base.py", line 656, in init_infant_single_anat_wf
anat_derivatives_wf = init_anat_derivatives_wf(
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/workflows/anatomical/outputs.py", line 510, in init_anat_derivatives_wf
(inputnode, raw_sources, [(source_files, 'in_files')]),
**UnboundLocalError: local variable 'raw_sources' referenced before assignment**
