Repository: cpp-lln-lab/bidsMReye (language: python)

Issue:
bidsmreye process only one task in the bids_dir
I want to run bidsmreye on fmriprep-preprocessed data. In the fmriprep-preprocessed data folder, I have three task: `task-wordLocalizer` `task-numMVPA` `task-aliceLocalizer`.  
When I run`bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant`, I only got results from `task-numMVPA`. If I specific the task to be processed by `bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant --task wordLocalizer`, I got an error `RuntimeError: Input dataset /Volumes/ssd/fmriprep does not have any data to process for filter
{this_filter}`

I put the full error message and the structure of bids_dir below
```
(base) yiyang@mac-ME22-048 ~ % bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant --task wordLocalizer
WARNING
[16:19:35] WARNING  bidsMReye - [16:19:35] - log level: WARNING                                                          bidsmreye.py:113
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/yiyang/miniforge3/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])                         │
│ ❱ 8 │   sys.exit(cli())                                                                          │
│   9                                                                                              │
│                                                                                                  │
│ ╭─────────────────────────────────────── locals ────────────────────────────────────────╮        │
│ │ __annotations__ = {}                                                                  │        │
│ │    __builtins__ = <module 'builtins' (built-in)>                                      │        │
│ │      __cached__ = None                                                                │        │
│ │         __doc__ = None                                                                │        │
│ │        __file__ = '/Users/yiyang/miniforge3/bin/bidsmreye'                            │        │
│ │      __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x1027d5000> │        │
│ │        __name__ = '__main__'                                                          │        │
│ │     __package__ = None                                                                │        │
│ │        __spec__ = None                                                                │        │
│ │             cli = <function cli at 0x2a149eb00>                                       │        │
│ │              re = <module 're' from '/Users/yiyang/miniforge3/lib/python3.10/re.py'>  │        │
│ │             sys = <module 'sys' (built-in)>                                           │        │
│ ╰───────────────────────────────────────────────────────────────────────────────────────╯        │
│                                                                                                  │
│ /Users/yiyang/DATA/bidsMReye/bidsmreye/bidsmreye.py:53 in cli                                    │
│                                                                                                  │
│    50 │   │   log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0))             │
│    51 │   log_level_name = log_levels()[log_level]                                               │
│    52 │                                                                                          │
│ ❱  53 │   bidsmreye(                                                                             │
│    54 │   │   bids_dir=args.bids_dir,                                                            │
│    55 │   │   output_dir=args.output_dir,                                                        │
│    56 │   │   analysis_level=args.analysis_level,                                                │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │           args = Namespace(bids_dir='/Volumes/ssd/fmriprep',                                 │ │
│ │                  output_dir='/Volumes/ssd/mreyeputput/localizer',                            │ │
│ │                  analysis_level='participant', action='all', participant_label=None,         │ │
│ │                  task=['wordLocalizer'], run=None, space=None, log_level=None, debug=False,  │ │
│ │                  reset_database=False, bids_filter_file=None, non_linear_coreg=False,        │ │
│ │                  model='1to6')                                                               │ │
│ │           argv = [                                                                           │ │
│ │                  │   '/Users/yiyang/miniforge3/bin/bidsmreye',                               │ │
│ │                  │   '/Volumes/ssd/fmriprep',                                                │ │
│ │                  │   '/Volumes/ssd/mreyeputput/localizer',                                   │ │
│ │                  │   'participant',                                                          │ │
│ │                  │   '--task',                                                               │ │
│ │                  │   'wordLocalizer'                                                         │ │
│ │                  ]                                                                           │ │
│ │      log_level = 2                                                                           │ │
│ │ log_level_name = 'WARNING'                                                                   │ │
│ │         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)                                                              │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /Users/yiyang/DATA/bidsMReye/bidsmreye/bidsmreye.py:127 in bidsmreye                             │
│                                                                                                  │
│   124 │   if action in {"all", "generalize"} and isinstance(cfg.model_weights_file, str):        │
│   125 │   │   cfg.model_weights_file = download(cfg.model_weights_file)                          │
│   126 │                                                                                          │
│ ❱ 127 │   dispatch(analysis_level=analysis_level, action=action, cfg=cfg)                        │
│   128                                                                                            │
│   129                                                                                            │
│   130 def dispatch(analysis_level: str, action: str, cfg: Config) -> None:                       │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │             action = 'all'                                                                   │ │
│ │     analysis_level = 'participant'                                                           │ │
│ │           bids_dir = '/Volumes/ssd/fmriprep'                                                 │ │
│ │        bids_filter = None                                                                    │ │
│ │   bids_filter_file = None                                                                    │ │
│ │                cfg = Config(                                                                 │ │
│ │                      │   input_dir=PosixPath('/Volumes/ssd/fmriprep'),                       │ │
│ │                      │                                                                       │ │
│ │                      output_dir=PosixPath('/Volumes/ssd/mreyeputput/localizer/bidsmreye'),   │ │
│ │                      │   subjects=[                                                          │ │
│ │                      │   │   '02',                                                           │ │
│ │                      │   │   '03',                                                           │ │
│ │                      │   │   '04',                                                           │ │
│ │                      │   │   '05',                                                           │ │
│ │                      │   │   '06',                                                           │ │
│ │                      │   │   '07',                                                           │ │
│ │                      │   │   '08',                                                           │ │
│ │                      │   │   '09',                                                           │ │
│ │                      │   │   '10',                                                           │ │
│ │                      │   │   '11',                                                           │ │
│ │                      │   │   ... +12                                                         │ │
│ │                      │   ],                                                                  │ │
│ │                      │   space=['MNI152NLin2009cAsym', 'T1w'],                               │ │
│ │                      │   task=['wordLocalizer'],                                             │ │
│ │                      │   run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +10],                       │ │
│ │                      │                                                                       │ │
│ │                      model_weights_file=PosixPath('/Users/yiyang/models/dataset_1to6.h5'),   │ │
│ │                      │   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 = 'WARNING'                                                               │ │
│ │ model_weights_file = '1to6'                                                                  │ │
│ │   non_linear_coreg = False                                                                   │ │
│ │         output_dir = '/Volumes/ssd/mreyeputput/localizer'                                    │ │
│ │  participant_label = None                                                                    │ │
│ │     reset_database = False                                                                   │ │
│ │                run = None                                                                    │ │
│ │              space = None                                                                    │ │
│ │               task = ['wordLocalizer']                                                       │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /Users/yiyang/DATA/bidsMReye/bidsmreye/bidsmreye.py:140 in dispatch                              │
│                                                                                                  │
│   137 │                                                                                          │
│   138 │   elif analysis_level == "participant":                                                  │
│   139 │   │   if action == "all":                                                                │
│ ❱ 140 │   │   │   prepare_data(cfg)                                                              │
│   141 │   │   │   generalize(cfg)                                                                │
│   142 │   │   elif action == "prepare":                                                          │
│   143 │   │   │   prepare_data(cfg)                                                              │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │         action = 'all'                                                                       │ │
│ │ analysis_level = 'participant'                                                               │ │
│ │            cfg = Config(                                                                     │ │
│ │                  │   input_dir=PosixPath('/Volumes/ssd/fmriprep'),                           │ │
│ │                  │   output_dir=PosixPath('/Volumes/ssd/mreyeputput/localizer/bidsmreye'),   │ │
│ │                  │   subjects=[                                                              │ │
│ │                  │   │   '02',                                                               │ │
│ │                  │   │   '03',                                                               │ │
│ │                  │   │   '04',                                                               │ │
│ │                  │   │   '05',                                                               │ │
│ │                  │   │   '06',                                                               │ │
│ │                  │   │   '07',                                                               │ │
│ │                  │   │   '08',                                                               │ │
│ │                  │   │   '09',                                                               │ │
│ │                  │   │   '10',                                                               │ │
│ │                  │   │   '11',                                                               │ │
│ │                  │   │   ... +12                                                             │ │
│ │                  │   ],                                                                      │ │
│ │                  │   space=['MNI152NLin2009cAsym', 'T1w'],                                   │ │
│ │                  │   task=['wordLocalizer'],                                                 │ │
│ │                  │   run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +10],                           │ │
│ │                  │   model_weights_file=PosixPath('/Users/yiyang/models/dataset_1to6.h5'),   │ │
│ │                  │   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                                                  │ │
│ │                  )                                                                           │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /Users/yiyang/DATA/bidsMReye/bidsmreye/prepare_data.py:178 in prepare_data                       │
│                                                                                                  │
│   175 │   │   config=["bids", "derivatives"],                                                    │
│   176 │   │   reset_database=cfg.reset_database,                                                 │
│   177 │   )                                                                                      │
│ ❱ 178 │   check_layout(cfg, layout_in)                                                           │
│   179 │                                                                                          │
│   180 │   layout_out = init_dataset(cfg)                                                         │
│   181                                                                                            │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │       cfg = Config(                                                                          │ │
│ │             │   input_dir=PosixPath('/Volumes/ssd/fmriprep'),                                │ │
│ │             │   output_dir=PosixPath('/Volumes/ssd/mreyeputput/localizer/bidsmreye'),        │ │
│ │             │   subjects=[                                                                   │ │
│ │             │   │   '02',                                                                    │ │
│ │             │   │   '03',                                                                    │ │
│ │             │   │   '04',                                                                    │ │
│ │             │   │   '05',                                                                    │ │
│ │             │   │   '06',                                                                    │ │
│ │             │   │   '07',                                                                    │ │
│ │             │   │   '08',                                                                    │ │
│ │             │   │   '09',                                                                    │ │
│ │             │   │   '10',                                                                    │ │
│ │             │   │   '11',                                                                    │ │
│ │             │   │   ... +12                                                                  │ │
│ │             │   ],                                                                           │ │
│ │             │   space=['MNI152NLin2009cAsym', 'T1w'],                                        │ │
│ │             │   task=['wordLocalizer'],                                                      │ │
│ │             │   run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +10],                                │ │
│ │             │   model_weights_file=PosixPath('/Users/yiyang/models/dataset_1to6.h5'),        │ │
│ │             │   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_in = BIDS Layout: .../Volumes/ssd/fmriprep | Subjects: 22 | Sessions: 46 | Runs: 430  │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /Users/yiyang/DATA/bidsMReye/bidsmreye/bids_utils.py:72 in check_layout                          │
│                                                                                                  │
│    69 │   )                                                                                      │
│    70 │                                                                                          │
│    71 │   if bf == []:                                                                           │
│ ❱  72 │   │   raise RuntimeError(                                                                │
│    73 │   │   │   f"Input dataset {layout.root} does not have "                                  │
│    74 │   │   │   "any data to process for filter\n{this_filter}"                                │
│    75 │   │   )                                                                                  │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │           bf = []                                                                            │ │
│ │          cfg = Config(                                                                       │ │
│ │                │   input_dir=PosixPath('/Volumes/ssd/fmriprep'),                             │ │
│ │                │   output_dir=PosixPath('/Volumes/ssd/mreyeputput/localizer/bidsmreye'),     │ │
│ │                │   subjects=[                                                                │ │
│ │                │   │   '02',                                                                 │ │
│ │                │   │   '03',                                                                 │ │
│ │                │   │   '04',                                                                 │ │
│ │                │   │   '05',                                                                 │ │
│ │                │   │   '06',                                                                 │ │
│ │                │   │   '07',                                                                 │ │
│ │                │   │   '08',                                                                 │ │
│ │                │   │   '09',                                                                 │ │
│ │                │   │   '10',                                                                 │ │
│ │                │   │   '11',                                                                 │ │
│ │                │   │   ... +12                                                               │ │
│ │                │   ],                                                                        │ │
│ │                │   space=['MNI152NLin2009cAsym', 'T1w'],                                     │ │
│ │                │   task=['wordLocalizer'],                                                   │ │
│ │                │   run=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +10],                             │ │
│ │                │   model_weights_file=PosixPath('/Users/yiyang/models/dataset_1to6.h5'),     │ │
│ │                │   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                                                    │ │
│ │                )                                                                             │ │
│ │         desc = {                                                                             │ │
│ │                │   'Name': 'fMRIPrep - fMRI PREProcessing workflow',                         │ │
│ │                │   'BIDSVersion': '1.4.0',                                                   │ │
│ │                │   'DatasetType': 'derivative',                                              │ │
│ │                │   'GeneratedBy': [                                                          │ │
│ │                │   │   {                                                                     │ │
│ │                │   │   │   'Name': 'fMRIPrep',                                               │ │
│ │                │   │   │   'Version': '23.1.4',                                              │ │
│ │                │   │   │   'CodeURL':                                                        │ │
│ │                'https://github.com/nipreps/fmriprep/archive/23.1.4.tar.gz'                   │ │
│ │                │   │   }                                                                     │ │
│ │                │   ],                                                                        │ │
│ │                │   'HowToAcknowledge': 'Please cite our paper                                │ │
│ │                (https://doi.org/10.1038/s41592-018-0235-4), and include t'+73,               │ │
│ │                │   'SourceDatasets': [{'URL': 'https://doi.org/doi:', 'DOI': 'doi:'}],       │ │
│ │                │   'License': ''                                                             │ │
│ │                }                                                                             │ │
│ │     for_file = 'bold'                                                                        │ │
│ │ generated_by = {                                                                             │ │
│ │                │   'Name': 'fMRIPrep',                                                       │ │
│ │                │   'Version': '23.1.4',                                                      │ │
│ │                │   'CodeURL': 'https://github.com/nipreps/fmriprep/archive/23.1.4.tar.gz'    │ │
│ │                }                                                                             │ │
│ │       layout = BIDS Layout: .../Volumes/ssd/fmriprep | Subjects: 22 | Sessions: 46 | Runs:   │ │
│ │                430                                                                           │ │
│ │  this_filter = {                                                                             │ │
│ │                │   'datatype': 'func',                                                       │ │
│ │                │   'desc': 'preproc',                                                        │ │
│ │                │   'suffix': '^bold$',                                                       │ │
│ │                │   'extension': 'nii.*',                                                     │ │
│ │                │   'task': ['wordLocalizer'],                                                │ │
│ │                │   'space': ['MNI152NLin2009cAsym', 'T1w'],                                  │ │
│ │                │   'run': [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... +10]                           │ │
│ │                }                                                                             │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
RuntimeError: Input dataset /Volumes/ssd/fmriprep does not have any data to process for filter
{this_filter}

```
```
(base) yiyang@mac-ME22-048 ~ % tree /Volumes/ssd/fmriprep/sub-02/ses-01/func                                         
/Volumes/ssd/fmriprep/sub-02/ses-01/func
├── sub-02_ses-01_task-aliceLocalizer_boldref.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_desc-confounds_timeseries.json
├── sub-02_ses-01_task-aliceLocalizer_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-aliceLocalizer_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-aliceLocalizer_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-aliceLocalizer_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-aliceLocalizer_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-aliceLocalizer_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-01_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-01_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-01_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-01_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-01_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-02_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-02_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-02_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-02_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-02_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-03_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-03_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-03_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-03_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-03_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-03_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-04_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-04_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-04_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-04_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-04_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-04_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-05_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-05_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-05_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-05_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-05_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-05_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-06_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-06_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-06_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-06_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-06_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-06_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-07_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-07_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-07_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-07_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-07_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-07_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-08_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-08_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-08_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-08_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-08_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-08_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_desc-confounds_timeseries.json
├── sub-02_ses-01_task-numMVPA_run-09_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-numMVPA_run-09_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-09_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-09_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-09_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-preproc_bold.json
├── sub-02_ses-01_task-numMVPA_run-09_space-T1w_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-wordLocalizer_boldref.nii.gz
├── sub-02_ses-01_task-wordLocalizer_desc-confounds_timeseries.json
├── sub-02_ses-01_task-wordLocalizer_desc-confounds_timeseries.tsv
├── sub-02_ses-01_task-wordLocalizer_from-T1w_to-scanner_mode-image_xfm.txt
├── sub-02_ses-01_task-wordLocalizer_from-scanner_to-T1w_mode-image_xfm.txt
├── sub-02_ses-01_task-wordLocalizer_from-scanner_to-boldref_mode-image_xfm.txt
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_boldref.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-brain_mask.json
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-preproc_bold.json
├── sub-02_ses-01_task-wordLocalizer_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-T1w_boldref.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-aparcaseg_dseg.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-aseg_dseg.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-brain_mask.json
├── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-brain_mask.nii.gz
├── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-preproc_bold.json
└── sub-02_ses-01_task-wordLocalizer_space-T1w_desc-preproc_bold.nii.gz

0 directories, 220 files



Discussion / hints:
We found the following entry in the [FAQ](https://bidsmreye.readthedocs.io/en/latest/FAQ.html) which you may find helpful:


- [How I should structure my input data?](https://bidsmreye.readthedocs.io/en/latest/FAQ.html#how-i-should-structure-my-input-data)

Feel free to close this issue if you found an answer in the FAQ. Otherwise, please give us a little time to review.

This is an automated reply, generated by [FAQtory](https://github.com/willmcgugan/faqtory)
I am not 100% sure as to what is going on here but I suspect that that it may be related to the pybids database.

Do you get the same errors if you run the commands with the `--reset_database` flag

```bash
bidsmreye /Volumes/ssd/fmriprep /Volumes/ssd/mreyeputput/localizer participant --action all --task wordLocalizer --reset_database
```
Will try to improve the error message and the FAQ to give better hints
unfortunately, it didn't solve the problem. New error messages are as below. It seems that bidsmreye are able to index all the three tasks ['aliceLocalizer', 'numMVPA', 'wordLocalizer'], but it can't process task 'aliceLocalizer' and 'wordLocalizer ' 
Do you have any idea about it?
```
RuntimeError: Input dataset /Volumes/ssd/fmriprep does not have any data to process 
for filter
{'datatype': 'func', 'desc': 'preproc', 'suffix': '^bold$', 'extension': 'nii.*', 
'task': ['wordLocalizer'], 'space': ['MNI152NLin2009cAsym', 'T1w'], 'run': [1, 2, 3, 
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]}.
This dataset contains subjects: ['02', '03', '04', '05', '06', '07', '08', '09', 
'10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 
'23'].This dataset contains tasks: ['aliceLocalizer', 'numMVPA', 'wordLocalizer'].Is 
your dataset a BIDS derivative dataset?
Check the FAQ for more information: 
https://bidsmreye.readthedocs.io/en/latest/FAQ.html
```
damn...

is the dataset on GIN by any chance? 

will make it easier for me to test things

not yet I have been putting off pushing my data to GIN... But now I have a good reason to do it. I'll let you know when it's done.
maybe start by pushing a couple of subjects only: should be enough for me to start testing

Hi, here's the data  https://gin.g-node.org/ying1234/fmriprep_demo
let me know if you have a problem accessing it.
looks I can access the data
will start downloading so I can test
Great! There's no rush so take your time.
I can reproduce the issue!!! 🎉 
and I think I spotted the issue

Fix patch:
diff --git a/bidsmreye/bids_utils.py b/bidsmreye/bids_utils.py
index 4e10bf3..434e011 100644
--- a/bidsmreye/bids_utils.py
+++ b/bidsmreye/bids_utils.py
@@ -17,7 +17,7 @@
 )
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.methods import methods
-from bidsmreye.utils import copy_license, create_dir_if_absent
+from bidsmreye.utils import copy_license, create_dir_if_absent, return_regex
 
 log = bidsmreye_log("bidsmreye")
 
@@ -60,9 +60,10 @@ def check_layout(cfg: Config, layout: BIDSLayout, for_file: str = "bold") -> Non
     if generated_by["Name"].lower() == "bidsmreye":
         this_filter = get_bids_filter_config()["mask"]
 
-    this_filter["task"] = cfg.task
+    this_filter["task"] = return_regex(cfg.task)
     this_filter["space"] = cfg.space
-    this_filter["run"] = cfg.run
+    if cfg.run:
+        this_filter["run"] = cfg.run
 
     log.debug(f"Looking for files with filter\n{this_filter}")
 
@@ -78,8 +79,8 @@ def check_layout(cfg: Config, layout: BIDSLayout, for_file: str = "bold") -> Non
         raise RuntimeError(
             f"Input dataset {layout.root} does not have "
             f"any data to process for filter\n{this_filter}.\n"
-            f"This dataset contains subjects: {subjects}."
-            f"This dataset contains tasks: {tasks}."
+            f"This dataset contains subjects: {subjects}.\n"
+            f"This dataset contains tasks: {tasks}.\n"
             "Is your dataset a BIDS derivative dataset?\n"
             "Check the FAQ for more information: "
             "https://bidsmreye.readthedocs.io/en/latest/FAQ.html"
diff --git a/bidsmreye/bidsmreye.py b/bidsmreye/bidsmreye.py
index 94bf70d..76c0a9e 100755
--- a/bidsmreye/bidsmreye.py
+++ b/bidsmreye/bidsmreye.py
@@ -102,14 +102,17 @@ def dispatch(analysis_level: str, action: str, cfg: Config) -> None:
 
             prepare_data(cfg)
             generalize(cfg)
+
         elif action == "prepare":
             from bidsmreye.prepare_data import prepare_data
 
             prepare_data(cfg)
+
         elif action == "generalize":
             from bidsmreye.generalize import generalize
 
             generalize(cfg)
+
         elif action == "qc":
             from bidsmreye.quality_control import quality_control_input
 
diff --git a/bidsmreye/configuration.py b/bidsmreye/configuration.py
index 213025b..f856731 100644
--- a/bidsmreye/configuration.py
+++ b/bidsmreye/configuration.py
@@ -105,8 +105,8 @@ def __attrs_post_init__(self) -> None:
 
         self.check_argument(attribute="subjects", layout_in=layout_in)
         self.check_argument(attribute="task", layout_in=layout_in)
-        self.check_argument(attribute="run", layout_in=layout_in)
         self.check_argument(attribute="space", layout_in=layout_in)
+        self.check_argument(attribute="run", layout_in=layout_in)
 
     def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
         """Check an attribute value compared to the input dataset content.
@@ -125,9 +125,15 @@ def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
         if attribute == "subjects":
             value = layout_in.get_subjects()
         elif attribute == "task":
-            value = layout_in.get_tasks()
+            value = layout_in.get_tasks(subject=self.subjects)
         elif attribute in {"space", "run"}:
-            value = layout_in.get(return_type="id", target=attribute, datatype="func")
+            value = layout_in.get(
+                return_type="id",
+                target=attribute,
+                datatype="func",
+                subject=self.subjects,
+                task=self.task,
+            )
 
         self.listify(attribute)
 
@@ -148,9 +154,12 @@ def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
                 )
             value = list(set(getattr(self, attribute)) & set(value))
 
-        setattr(self, attribute, value)
-
         # run and space can be empty if their entity are not used
+        # we will figure out the values for run
+        # in subject / task wise manner later on
+        if attribute not in ["run"]:
+            setattr(self, attribute, value)
+
         if attribute not in ["run", "space"] and not getattr(self, attribute):
             raise RuntimeError(f"No {attribute} found in {self.input_dir}")
 
diff --git a/docs/source/CHANGELOG.md b/docs/source/CHANGELOG.md
index db7e6dd..0c926a0 100644
--- a/docs/source/CHANGELOG.md
+++ b/docs/source/CHANGELOG.md
@@ -31,6 +31,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* [FIX] do not apply run found for one task to all tasks by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/228
+
 ### Security
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 7a5b0ab..69de0c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ dependencies = [
     "kaleido",
     "pooch>=1.6.0",
     "pybids",
+    "antspyx<0.5",
     "tqdm",
     "tomli; python_version < '3.11'",
     "keras<3.0.0",
diff --git a/requirements.txt b/requirements.txt
index d656165..68ae0d1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,7 +9,9 @@ absl-py==2.1.0
     #   tensorboard
     #   tensorflow
 antspyx==0.4.2
-    # via deepmreye
+    # via
+    #   bidsmreye (pyproject.toml)
+    #   deepmreye
 anyio==4.4.0
     # via
     #   httpx
@@ -430,6 +432,8 @@ rfc3986-validator==0.1.1
     #   jsonschema
     #   jupyter-events
 rich==13.7.1
+    # via rich-argparse
+rich-argparse==1.5.2
     # via bidsmreye (pyproject.toml)
 rpds-py==0.19.1
     # via


Test patch:
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 67c50d5..702461d 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -87,7 +87,6 @@ def test_set_this_filter_bold(pybids_test_dataset, output_dir):
         "datatype": "func",
         "desc": "preproc",
         "extension": "nii.*",
-        "run": "1|2",
         "subject": "001",
         "suffix": "^bold$",
     }