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cpp-lln-lab / bidsMReye

BIDS app using deepMReye to decode eye motion for fMRI time series data.
https://bidsmreye.readthedocs.io/en/latest/
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[BUG] No Subject Found in Layout #170

Open Michael-Sun opened 9 months ago

Michael-Sun commented 9 months ago

Is there an existing issue for this?

Expected Behavior

BidsMReye detects the subject and processes it.

Current Behavior

BIDSLayout cannot seem to find the subject SID001641, despite it being present.

Error message

2023-09-19 07:53:32.635559: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/var/spool/slurmd/job7733469/slurm_script: line 61: 16097 Killed                  bidsmreye --action all ${bids_dir} ${output_dir} participant --participant_label ${SUBJ} --space MNI152NLin2009cAsym -v
2023-09-19 08:11:39.456997: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
+------------------------------- Traceback (most recent call last) --------------------------------+
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/bin/bidsmreye:8 in <module>       |
|                                                                                                  |
|   5 from bidsmreye.bidsmreye import cli                                                          |
|   6 if __name__ == '__main__':                                                                   |
|   7     sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                         |
| \u2771 8     sys.exit(cli())                                                                          |
|   9                                                                                              |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| | cli = <function cli at 0x2b41fce1f0d0>                                                       | |
| |  re = <module 're' from                                                                      | |
| |       '/dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/re.py'>  | |
| | sys = <module 'sys' (built-in)>                                                              | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/bidsmreye.py:54 in cli                                                                      |
|                                                                                                  |
|    51         log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0))             |
|    52     log_level_name = log_levels()[log_level]                                               |
|    53                                                                                            |
| \u2771  54     bidsmreye(                                                                             |
|    55         bids_dir=args.bids_dir,                                                            |
|    56         output_dir=args.output_dir,                                                        |
|    57         analysis_level=args.analysis_level,                                                |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| |     adjustment = -1                                                                          | |
| |           args = Namespace(bids_dir='/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/deriva\u2026 | |
| |                  output_dir='/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/de\u2026 | |
| |                  analysis_level='group', action='qc', participant_label=['SID001641'],       | |
| |                  task=None, run=None, space=['MNI152NLin2009cAsym'], log_level=[-1],         | |
| |                  debug=False, reset_database=False, bids_filter_file=None,                   | |
| |                  non_linear_coreg=False, model='1to6')                                       | |
| |           argv = [                                                                           | |
| |                      '/dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/bin/bi\u2026 | |
| |                      '--action',                                                             | |
| |                      'qc',                                                                   | |
| |                      '/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/fmriprep-\u2026 | |
| |                      '/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/deepmreye\u2026 | |
| |                      'group',                                                                | |
| |                      '--participant_label',                                                  | |
| |                      'SID001641',                                                            | |
| |                      '--space',                                                              | |
| |                      'MNI152NLin2009cAsym',                                                  | |
| |                      ... +1                                                                  | |
| |                  ]                                                                           | |
| |      log_level = 1                                                                           | |
| | log_level_name = 'INFO'                                                                      | |
| |         parser = MuhParser(prog='bidsmreye', usage=None, description='BIDS app using         | |
| |                  deepMReye to decode eye motion for fMRI time series data.',                 | |
| |                  formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', | |
| |                  add_help=True)                                                              | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/bidsmreye.py:129 in bidsmreye                                                               |
|                                                                                                  |
|   126     if action in {"all", "generalize"} and isinstance(cfg.model_weights_file, str):        |
|   127         cfg.model_weights_file = download(cfg.model_weights_file)                          |
|   128                                                                                            |
| \u2771 129     dispatch(analysis_level=analysis_level, action=action, cfg=cfg)                        |
|   130                                                                                            |
|   131                                                                                            |
|   132 def dispatch(analysis_level: str, action: str, cfg: Config) -> None:                       |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| |             action = 'qc'                                                                    | |
| |     analysis_level = 'group'                                                                 | |
| |           bids_dir = '/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/fmriprep-\u2026 | |
| |        bids_filter = None                                                                    | |
| |   bids_filter_file = None                                                                    | |
| |                cfg = Config(                                                                 | |
| |                          input_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASA\u2026 | |
| |                          output_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WAS\u2026 | |
| |                          subjects=['SID001641'],                                             | |
| |                          space=['MNI152NLin2009cAsym'],                                      | |
| |                          task=[                                                              | |
| |                              'movemap',                                                      | |
| |                              'pinellocalizer',                                               | |
| |                              'bodymapST2',                                                   | |
| |                              'hyperalignment',                                               | |
| |                              'bodymapST1',                                                   | |
| |                              'distractmap',                                                  | |
| |                              'acceptmapXexperience',                                         | |
| |                              'acceptmapXregulate',                                           | |
| |                              'acceptmap1Xexperience',                                        | |
| |                              'acceptmap1Xpostexp',                                           | |
| |                              ... +5                                                          | |
| |                          ],                                                                  | |
| |                          run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +3],                        | |
| |                          model_weights_file='1to6',                                          | |
| |                          bids_filter={                                                       | |
| |                              'bold': {                                                       | |
| |                                  'datatype': 'func',                                         | |
| |                                  'desc': 'preproc',                                          | |
| |                                  'suffix': '^bold$',                                         | |
| |                                  'extension': 'nii.*'                                        | |
| |                              },                                                              | |
| |                              'mask': {'suffix': 'mask', 'extension': 'p'},                   | |
| |                              'no_label': {                                                   | |
| |                                  'desc': 'nolabel',                                          | |
| |                                  'suffix': '^bidsmreye$$',                                   | |
| |                                  'extension': 'npz'                                          | |
| |                              },                                                              | |
| |                              'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'},      | |
| |                              'eyetrack_qc': {'suffix': '^eyetrack$$', 'extension': 'json'}   | |
| |                          },                                                                  | |
| |                          debug=False,                                                        | |
| |                          reset_database=False,                                               | |
| |                          non_linear_coreg=False                                              | |
| |                      )                                                                       | |
| |              debug = False                                                                   | |
| |     log_level_name = 'INFO'                                                                  | |
| | model_weights_file = '1to6'                                                                  | |
| |   non_linear_coreg = False                                                                   | |
| |         output_dir = '/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/deepmreye' | |
| |  participant_label = ['SID001641']                                                           | |
| |     reset_database = False                                                                   | |
| |                run = None                                                                    | |
| |              space = ['MNI152NLin2009cAsym']                                                 | |
| |               task = None                                                                    | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/bidsmreye.py:135 in dispatch                                                                |
|                                                                                                  |
|   132 def dispatch(analysis_level: str, action: str, cfg: Config) -> None:                       |
|   133     if analysis_level == "group":                                                          |
|   134         if action == "qc":                                                                 |
| \u2771 135             group_report(cfg=cfg)                                                          |
|   136         else:                                                                              |
|   137             log.error("Unknown group level action")                                        |
|   138             sys.exit(1)                                                                    |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| |         action = 'qc'                                                                        | |
| | analysis_level = 'group'                                                                     | |
| |            cfg = Config(                                                                     | |
| |                      input_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/d\u2026 | |
| |                      output_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/\u2026 | |
| |                      subjects=['SID001641'],                                                 | |
| |                      space=['MNI152NLin2009cAsym'],                                          | |
| |                      task=[                                                                  | |
| |                          'movemap',                                                          | |
| |                          'pinellocalizer',                                                   | |
| |                          'bodymapST2',                                                       | |
| |                          'hyperalignment',                                                   | |
| |                          'bodymapST1',                                                       | |
| |                          'distractmap',                                                      | |
| |                          'acceptmapXexperience',                                             | |
| |                          'acceptmapXregulate',                                               | |
| |                          'acceptmap1Xexperience',                                            | |
| |                          'acceptmap1Xpostexp',                                               | |
| |                          ... +5                                                              | |
| |                      ],                                                                      | |
| |                      run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +3],                            | |
| |                      model_weights_file='1to6',                                              | |
| |                      bids_filter={                                                           | |
| |                          'bold': {                                                           | |
| |                              'datatype': 'func',                                             | |
| |                              'desc': 'preproc',                                              | |
| |                              'suffix': '^bold$',                                             | |
| |                              'extension': 'nii.*'                                            | |
| |                          },                                                                  | |
| |                          'mask': {'suffix': 'mask', 'extension': 'p'},                       | |
| |                          'no_label': {                                                       | |
| |                              'desc': 'nolabel',                                              | |
| |                              'suffix': '^bidsmreye$$',                                       | |
| |                              'extension': 'npz'                                              | |
| |                          },                                                                  | |
| |                          'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'},          | |
| |                          'eyetrack_qc': {'suffix': '^eyetrack$$', 'extension': 'json'}       | |
| |                      },                                                                      | |
| |                      debug=False,                                                            | |
| |                      reset_database=False,                                                   | |
| |                      non_linear_coreg=False                                                  | |
| |                  )                                                                           | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/visualize.py:140 in group_report                                                            |
|                                                                                                  |
|   137     :return: Figure object                                                                 |
|   138     :rtype: Any                                                                            |
|   139     """                                                                                    |
| \u2771 140     qc_data = collect_group_qc_data(cfg)                                                   |
|   141                                                                                            |
|   142     fig = go.FigureWidget(                                                                 |
|   143         make_subplots(                                                                     |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| | cfg = Config(                                                                                | |
| |           input_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/\u2026 | |
| |           output_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives\u2026 | |
| |           subjects=['SID001641'],                                                            | |
| |           space=['MNI152NLin2009cAsym'],                                                     | |
| |           task=[                                                                             | |
| |               'movemap',                                                                     | |
| |               'pinellocalizer',                                                              | |
| |               'bodymapST2',                                                                  | |
| |               'hyperalignment',                                                              | |
| |               'bodymapST1',                                                                  | |
| |               'distractmap',                                                                 | |
| |               'acceptmapXexperience',                                                        | |
| |               'acceptmapXregulate',                                                          | |
| |               'acceptmap1Xexperience',                                                       | |
| |               'acceptmap1Xpostexp',                                                          | |
| |               ... +5                                                                         | |
| |           ],                                                                                 | |
| |           run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +3],                                       | |
| |           model_weights_file='1to6',                                                         | |
| |           bids_filter={                                                                      | |
| |               'bold': {                                                                      | |
| |                   'datatype': 'func',                                                        | |
| |                   'desc': 'preproc',                                                         | |
| |                   'suffix': '^bold$',                                                        | |
| |                   'extension': 'nii.*'                                                       | |
| |               },                                                                             | |
| |               'mask': {'suffix': 'mask', 'extension': 'p'},                                  | |
| |               'no_label': {                                                                  | |
| |                   'desc': 'nolabel',                                                         | |
| |                   'suffix': '^bidsmreye$$',                                                  | |
| |                   'extension': 'npz'                                                         | |
| |               },                                                                             | |
| |               'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'},                     | |
| |               'eyetrack_qc': {'suffix': '^eyetrack$$', 'extension': 'json'}                  | |
| |           },                                                                                 | |
| |           debug=False,                                                                       | |
| |           reset_database=False,                                                              | |
| |           non_linear_coreg=False                                                             | |
| |       )                                                                                      | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/visualize.py:56 in collect_group_qc_data                                                    |
|                                                                                                  |
|    53     """                                                                                    |
|    54     layout = get_dataset_layout(cfg.output_dir, use_database=False)                        |
|    55                                                                                            |
| \u2771  56     subjects = list_subjects(cfg, layout)                                                  |
|    57                                                                                            |
|    58     this_filter = set_this_filter(cfg, subjects, "eyetrack_qc")                            |
|    59                                                                                            |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| |    cfg = Config(                                                                             | |
| |              input_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivativ\u2026 | |
| |              output_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivati\u2026 | |
| |              subjects=['SID001641'],                                                         | |
| |              space=['MNI152NLin2009cAsym'],                                                  | |
| |              task=[                                                                          | |
| |                  'movemap',                                                                  | |
| |                  'pinellocalizer',                                                           | |
| |                  'bodymapST2',                                                               | |
| |                  'hyperalignment',                                                           | |
| |                  'bodymapST1',                                                               | |
| |                  'distractmap',                                                              | |
| |                  'acceptmapXexperience',                                                     | |
| |                  'acceptmapXregulate',                                                       | |
| |                  'acceptmap1Xexperience',                                                    | |
| |                  'acceptmap1Xpostexp',                                                       | |
| |                  ... +5                                                                      | |
| |              ],                                                                              | |
| |              run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +3],                                    | |
| |              model_weights_file='1to6',                                                      | |
| |              bids_filter={                                                                   | |
| |                  'bold': {                                                                   | |
| |                      'datatype': 'func',                                                     | |
| |                      'desc': 'preproc',                                                      | |
| |                      'suffix': '^bold$',                                                     | |
| |                      'extension': 'nii.*'                                                    | |
| |                  },                                                                          | |
| |                  'mask': {'suffix': 'mask', 'extension': 'p'},                               | |
| |                  'no_label': {                                                               | |
| |                      'desc': 'nolabel',                                                      | |
| |                      'suffix': '^bidsmreye$$',                                               | |
| |                      'extension': 'npz'                                                      | |
| |                  },                                                                          | |
| |                  'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'},                  | |
| |                  'eyetrack_qc': {'suffix': '^eyetrack$$', 'extension': 'json'}               | |
| |              },                                                                              | |
| |              debug=False,                                                                    | |
| |              reset_database=False,                                                           | |
| |              non_linear_coreg=False                                                          | |
| |          )                                                                                   | |
| | layout = BIDS Layout: ...erivatives/deepmreye/bidsmreye | Subjects: 10 | Sessions: 73 |      | |
| |          Runs: 49                                                                            | |
| +----------------------------------------------------------------------------------------------+ |
|                                                                                                  |
| /dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/deepmreye/lib/python3.9/site-packages/bidsm |
| reye/bids_utils.py:244 in list_subjects                                                          |
|                                                                                                  |
|   241     subjects = layout.get(return_type="id", target="subject", subject=cfg.subjects)        |
|   242                                                                                            |
|   243     if subjects == [] or subjects is None:                                                 |
| \u2771 244         raise RuntimeError(f"No subject found in layout:\n\t{layout.root}")                |
|   245                                                                                            |
|   246     if cfg.debug:                                                                          |
|   247         subjects = [subjects[0]]                                                           |
|                                                                                                  |
| +------------------------------------------- locals -------------------------------------------+ |
| |      cfg = Config(                                                                           | |
| |                input_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivat\u2026 | |
| |                output_dir=PosixPath('/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/deriva\u2026 | |
| |                subjects=['SID001641'],                                                       | |
| |                space=['MNI152NLin2009cAsym'],                                                | |
| |                task=[                                                                        | |
| |                    'movemap',                                                                | |
| |                    'pinellocalizer',                                                         | |
| |                    'bodymapST2',                                                             | |
| |                    'hyperalignment',                                                         | |
| |                    'bodymapST1',                                                             | |
| |                    'distractmap',                                                            | |
| |                    'acceptmapXexperience',                                                   | |
| |                    'acceptmapXregulate',                                                     | |
| |                    'acceptmap1Xexperience',                                                  | |
| |                    'acceptmap1Xpostexp',                                                     | |
| |                    ... +5                                                                    | |
| |                ],                                                                            | |
| |                run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +3],                                  | |
| |                model_weights_file='1to6',                                                    | |
| |                bids_filter={                                                                 | |
| |                    'bold': {                                                                 | |
| |                        'datatype': 'func',                                                   | |
| |                        'desc': 'preproc',                                                    | |
| |                        'suffix': '^bold$',                                                   | |
| |                        'extension': 'nii.*'                                                  | |
| |                    },                                                                        | |
| |                    'mask': {'suffix': 'mask', 'extension': 'p'},                             | |
| |                    'no_label': {                                                             | |
| |                        'desc': 'nolabel',                                                    | |
| |                        'suffix': '^bidsmreye$$',                                             | |
| |                        'extension': 'npz'                                                    | |
| |                    },                                                                        | |
| |                    'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'},                | |
| |                    'eyetrack_qc': {'suffix': '^eyetrack$$', 'extension': 'json'}             | |
| |                },                                                                            | |
| |                debug=False,                                                                  | |
| |                reset_database=False,                                                         | |
| |                non_linear_coreg=False                                                        | |
| |            )                                                                                 | |
| |   layout = BIDS Layout: ...erivatives/deepmreye/bidsmreye | Subjects: 10 | Sessions: 73 |    | |
| |            Runs: 49                                                                          | |
| | subjects = []                                                                                | |
| +----------------------------------------------------------------------------------------------+ |
+--------------------------------------------------------------------------------------------------+
RuntimeError: No subject found in layout:
        /dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/deepmreye/bidsmreye

Environment

- OS: CentOS Linux release 7.9.2009 (Core)

Branch

No response

Anything else?

No response

github-actions[bot] commented 9 months ago

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

Michael-Sun commented 8 months ago

This issue is caused by a prematurely accessed pybids directory which is created by early iterations in a parallelized batch. Better practice would be to pre-create a pybids directory before invoking bidsmreye in parallel.