[BUG] No Subject Found in Layout #170
Description
Is there an existing issue for this?
- I have searched the existing issues
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