BIDS Structure and Entities

For file querying to work in TimeseriesExtractor.get_bold, the dataset must in a BIDS compliant structure such as the following examples:

• Basic BIDS directory

  bids_root/
  ├── dataset_description.json
  ├── sub-<subject_label>/
  │   └── func/
  │       ├── *events.tsv
          └── *bold.json
  ├── derivatives/
  │   └── fmriprep-<version_label>/
  │       ├── dataset_description.json
  │       └── sub-<subject_label>/
  │           └── func/
  │               ├── *confounds_timeseries.tsv
  │               ├── *brain_mask.nii.gz
  │               └── *preproc_bold.nii.gz
  

• BIDS directory with session-level organization

  bids_root/
  ├── dataset_description.json
  ├── sub-<subject_label>/
  │   └── ses-<session_label>/
  │       └── func/
  │           ├── *events.tsv
              └── *bold.json
  ├── derivatives/
  │   └── fmriprep-<version_label>/
  │       ├── dataset_description.json
  │       └── sub-<subject_label>/
  │           └── ses-<session_label>/
  │               └── func/
  │                   ├── *confounds_timeseries.tsv
  │                   ├── *brain_mask.nii.gz
  │                   └── *preproc_bold.nii.gz
  

Note: Only the preprocessed BOLD file is required. Additional files such as the confounds tsv (needed for denoising), mask, and task timing tsv file (needed for filtering a specific task condition) depend on the specific analyses.

Entities

All preprocessed bold related files within the pipeline folder must have the “sub-”, “task-”, and “desc-” entities (key-value pairs within filenames) in their names. The preprocessed bold and brain mask files must include the “space-” entity in their names. Files in the raw directory, require the “sub-” and “task-” entities.

Examples of minimum required naming scheme for each file:

• Files in derivatives folder

"sub-01_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
"sub-01_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
"sub-01_task-rest_desc-confounds_timeseries.tsv"
"sub-01_task-rest_desc-confounds_timeseries.json"

• Files in the raw directory

"sub-01_task-rest_events.tsv"
"sub-01_task-rest_bold.json"

Note: The “ses-” and “run-” entities should be included if specifying a run or session.