"np" not defined

[smeisler]

What version of fMRIPrep are you using?

21.0.0rc0

What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"?

Singularity (3.6.3) on Linux HPC

What is the exact command-line you used?

singularity run -B ${scratch} -B ${bids_dir} $IMG ${bids_dir} ${output_dir} participant --participant_label ${subject:4} \
-w $scratch --fs-license-file $license --ignore fieldmaps --mem_mb 39500 --use-syn-sdc --force-syn \
--skip-bids-validation --use-aroma --cifti-output 91k \
--output-spaces MNIPediatricAsym:cohort-1 T1w MNI152NLin6Asym MNI152NLin2009cAsym

Have you checked that your inputs are BIDS valid?

Yes (OpenNeuro ds003604)

Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?

No

Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?

210915-15:36:23,976 nipype.workflow IMPORTANT:
	 Building fMRIPrep's workflow:
           * BIDS dataset path: /om4/group/gablab/data/ds003604.
           * Participant list: ['5002'].
           * Run identifier: 20210915-151951_359f75f4-363f-4879-a91f-dc4319eb776d.
           * Output spaces: MNIPediatricAsym:cohort-1:res-native T1w MNI152NLin6Asym:res-native MNI152NLin2009cAsym:res-native.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /om4/group/gablab/data/ds003604/derivatives/freesurfer.
210915-15:36:29,480 nipype.workflow CRITICAL:
	 SyN processing is not yet implemented.
210915-15:36:29,759 nipype.workflow INFO:
	 No single-band-reference found for sub-5002_ses-5_task-Gram_acq-D1S11_run-01_bold.nii.gz.
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.8/site-packages/fmriprep/cli/workflow.py", line 118, in build_workflow
    retval["workflow"] = init_fmriprep_wf()
  File "/usr/local/miniconda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 85, in init_fmriprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/usr/local/miniconda/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 349, in init_single_subject_wf
    func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap)
  File "/usr/local/miniconda/lib/python3.8/site-packages/fmriprep/workflows/bold/base.py", line 446, in init_func_preproc_wf
    bold_stc_wf = init_bold_stc_wf(name='bold_stc_wf', metadata=metadata)
  File "/usr/local/miniconda/lib/python3.8/site-packages/fmriprep/workflows/bold/stc.py", line 99, in init_bold_stc_wf
    tzero = np.round(first + frac * (last - first), 3)
NameError: name 'np' is not defined

Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?

Yes (previous recon-all outputs)

fMRIPrep log

Included in the traceback

[effigies]

Duplicate of #2532. Fixed in #2533. We plan to release another RC in the next day or two. In the meantime, you can use nipreps/fmriprep:unstable.