COPYING DATA TO SCRATCH
Submitted job for: sub-002
$'Command :\n'singularity run --writable-tmpfs -e -B /om2/scratch/tmp/treves/jhana_fmriprep/sub-002,/om2/user/treves/.cache /om2/user/treves/software/qsiprep-0.22.1.sif /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/ participant --participant_label sub-002 -w /om2/scratch/tmp/treves/jhana_fmriprep/sub-002 --fs-license-file /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/code/license.txt --unringing_method mrdegibbs --ignore fieldmaps --output_resolution 1.25 --stop-on-first-crash --notrack  --mem-mb 31500 --nthreads 16 --omp-nthreads 8 --recon-spec mrtrix_multishell_msmt_ACT-hsvs --skip_bids_validation --freesurfer-input /nese/mit/group/gablab/data/JhanaGroup/derivatives2/sub-002 --recon-only --recon-input /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep
240910-10:10:35,855 nipype.workflow INFO:
	 Running recon-only mode: --recon-input was used.
240910-10:10:35,856 nipype.workflow WARNING:
	 Argument --recon-only is not needed if --recon-input is specified.
240910-10:10:35,857 nipype.workflow IMPORTANT:
	 Running QSIRecon version 0.22.2.dev0+g712047b.d20240802

         License NOTICE ##################################################
         QSIPrep 0.22.2.dev0+g712047b.d20240802
         Copyright The PennLINC Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
240910-10:10:36,457 nipype.workflow IMPORTANT:
	 Building QSIRecon's workflow:
           * BIDS dataset path: /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data.
           * Participant list: ['002'].
           * Run identifier: 20240910-101009_2b080ac1-d8b2-4aa9-b334-2b9d750b7904.
240910-10:10:36,727 nipype.workflow INFO:
	 found ['/om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep/sub-002/dwi/sub-002_space-T1w_desc-preproc_dwi.nii.gz'] in /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep
240910-10:10:36,733 nipype.workflow INFO:
	 CHECKING /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep/sub-002/anat/sub-002_desc-brain_mask.nii.gz: True
240910-10:10:36,735 nipype.workflow INFO:
	 CHECKING /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep/sub-002/anat/sub-002_desc-preproc_T1w.nii.gz: True
240910-10:10:36,735 nipype.workflow INFO:
	 Found usable QSIPrep-preprocessed T1w image and mask.
240910-10:10:36,736 nipype.workflow INFO:
	 CHECKING /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep/sub-002/anat/sub-002_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5: True
240910-10:10:36,736 nipype.workflow INFO:
	 CHECKING /om2/scratch/tmp/treves/jhana_fmriprep/sub-002/data/derivatives_qsi/qsiprep/sub-002/anat/sub-002_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5: True
240910-10:10:36,736 nipype.workflow INFO:
	 Found high-res anatomical data in preprocessed inputs for 002.
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/workflow.py", line 160, in build_workflow
    retval["workflow"] = workflow_builder()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 72, in init_qsirecon_wf
    single_subject_wf = init_single_subject_recon_wf(subject_id=subject_id)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 153, in init_single_subject_recon_wf
    anat_ingress_node, available_anatomical_data = init_highres_recon_anatomical_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/recon/anatomical.py", line 143, in init_highres_recon_anatomical_wf
    missing_fs_hsvs_files = check_hsv_inputs(Path(subject_freesurfer_path))
  File "/opt/conda/envs/qsiprep/lib/python3.10/pathlib.py", line 960, in __new__
    self = cls._from_parts(args)
  File "/opt/conda/envs/qsiprep/lib/python3.10/pathlib.py", line 594, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/opt/conda/envs/qsiprep/lib/python3.10/pathlib.py", line 578, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType