diff --git a/patch-bids-tables.sql b/patch-bids-tables.sql
new file mode 100644
index 000000000..a9c9ef07d
--- /dev/null
+++ b/patch-bids-tables.sql
@@ -0,0 +1,52 @@
+CREATE TABLE `bids_dataset` (
+  `ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  `Path` VARCHAR(255) NOT NULL,
+  `InsertTime` DATETIME NOT NULL,
+  PRIMARY KEY (`ID`),
+  UNIQUE KEY `bids_dataset_path_unique` (`Path`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
+
+CREATE TABLE `bids_file` (
+  `ID` INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  `DatasetID` INT(10) UNSIGNED NOT NULL,
+  `Path` VARCHAR(255) NOT NULL,
+  `SourcePath` VARCHAR(255) NULL,
+  `InsertTime` DATETIME NOT NULL,
+  `Blake2bHash` CHAR(128) NOT NULL,
+  `Derivative` TINYINT(1) NOT NULL,
+  PRIMARY KEY (`ID`),
+  UNIQUE KEY `bids_file_path_unique` (`Path`),
+  KEY `bids_file_dataset_id_fk_idx` (`DatasetID`),
+  CONSTRAINT `bids_file_dataset_id_fk`
+    FOREIGN KEY (`DatasetID`) REFERENCES `bids_dataset` (`ID`) ON DELETE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
+
+ALTER TABLE `files`
+  ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
+  ADD KEY `files_bids_info_id_fk_idx` (`BidsInfoID`),
+  ADD CONSTRAINT `files_bids_info_id_fk`
+    FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;
+
+ALTER TABLE `physiological_file`
+  ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
+  ADD KEY `physiological_file_bids_info_id_fk_idx` (`BidsInfoID`),
+  ADD CONSTRAINT `physiological_file_bids_info_id_fk`
+    FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;
+
+ALTER TABLE `physiological_event_file`
+  ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
+  ADD KEY `physiological_event_file_bids_info_id_fk_idx` (`BidsInfoID`),
+  ADD CONSTRAINT `physiological_event_file_bids_info_id_fk`
+    FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;
+
+ALTER TABLE `meg_ctf_head_shape_file`
+  ADD COLUMN `BidsInfoID` INT(10) UNSIGNED NULL,
+  ADD COLUMN `InsertTime` DATETIME NOT NULL,
+  ADD KEY `meg_ctf_head_shape_file_bids_info_id_fk_idx` (`BidsInfoID`),
+  ADD CONSTRAINT `meg_ctf_head_shape_file_bids_info_id_fk`
+    FOREIGN KEY (`BidsInfoID`) REFERENCES `bids_file` (`ID`) ON DELETE SET NULL;
+
+ALTER TABLE `physiological_file`
+  DROP FOREIGN KEY `physiological_file_head_shape_file_id_fk`,
+  ADD CONSTRAINT `physiological_file_head_shape_file_id_fk`
+    FOREIGN KEY (`HeadShapeFileID`) REFERENCES `meg_ctf_head_shape_file` (`ID`) ON DELETE SET NULL;
diff --git a/python/lib/db/models/bids_dataset.py b/python/lib/db/models/bids_dataset.py
new file mode 100644
index 000000000..7121b253e
--- /dev/null
+++ b/python/lib/db/models/bids_dataset.py
@@ -0,0 +1,30 @@
+from datetime import datetime
+from pathlib import Path
+
+from sqlalchemy.orm import Mapped, mapped_column
+
+from lib.db.base import Base
+from lib.db.decorators.string_path import StringPath
+
+
+class DbBidsDataset(Base):
+    """
+    A LORIS BIDS dataset.
+    """
+
+    __tablename__ = 'bids_dataset'
+
+    id: Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True)
+    """
+    The ID of this BIDS dataset.
+    """
+
+    path: Mapped[Path] = mapped_column('Path', StringPath, unique=True)
+    """
+    The path of this BIDS dataset, relative to the LORIS data directory.
+    """
+
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this BIDS dataset was created in LORIS.
+    """
diff --git a/python/lib/db/models/bids_file.py b/python/lib/db/models/bids_file.py
new file mode 100644
index 000000000..6c0530039
--- /dev/null
+++ b/python/lib/db/models/bids_file.py
@@ -0,0 +1,58 @@
+from datetime import datetime
+from pathlib import Path
+
+from sqlalchemy import ForeignKey
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+import lib.db.models.bids_dataset as db_bids_dataset
+from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
+from lib.db.decorators.string_path import StringPath
+
+
+class DbBidsFile(Base):
+    """
+    A file within a LORIS BIDS dataset.
+    """
+
+    __tablename__ = 'bids_file'
+
+    id: Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True)
+    """
+    The ID of this BIDS file.
+    """
+
+    dataset_id: Mapped[int] = mapped_column('DatasetID', ForeignKey('bids_dataset.ID', ondelete='CASCADE'))
+    """
+    The ID of the BIDS dataset to which this file belongs.
+    """
+
+    path: Mapped[Path] = mapped_column('Path', StringPath, unique=True)
+    """
+    The path of this file relative to its LORIS BIDS dataset.
+    """
+
+    source_path: Mapped[Path | None] = mapped_column('SourcePath', StringPath)
+    """
+    The source path of this file relative to the BIDS dataset from which it was imported.
+    """
+
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this BIDS dataset was created in LORIS.
+    """
+
+    blake2b_hash: Mapped[str] = mapped_column('Blake2bHash')
+    """
+    The BLAKE2b hash of this file.
+    """
+
+    derivative: Mapped[bool] = mapped_column('Derivative', IntBool)
+    """
+    Whether this file is a BIDS derivative.
+    """
+
+    dataset: Mapped['db_bids_dataset.DbBidsDataset'] = relationship('DbBidsDataset')
+    """
+    The BIDS dataset to which this file belongs.
+    """
diff --git a/python/lib/db/models/file.py b/python/lib/db/models/file.py
index ceb5599eb..04ae55011 100644
--- a/python/lib/db/models/file.py
+++ b/python/lib/db/models/file.py
@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.dicom_archive as db_dicom_archive
 import lib.db.models.file_parameter as db_file_parameter
 import lib.db.models.session as db_session
@@ -40,6 +41,16 @@ class DbFile(Base):
     acquisition_order_per_modality : Mapped[int | None]   = mapped_column('AcqOrderPerModality')
     acquisition_date               : Mapped[date | None]  = mapped_column('AcquisitionDate')
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this file, if any.
+    """
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this file, if any.
+    """
+
     session: Mapped['db_session.DbSession'] = relationship('DbSession', back_populates='files')
     """
     The session to which this file belongs.
diff --git a/python/lib/db/models/meg_ctf_head_shape_file.py b/python/lib/db/models/meg_ctf_head_shape_file.py
index 186d34504..7aca80499 100644
--- a/python/lib/db/models/meg_ctf_head_shape_file.py
+++ b/python/lib/db/models/meg_ctf_head_shape_file.py
@@ -1,7 +1,10 @@
+from datetime import datetime
 from pathlib import Path
 
+from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.meg_ctf_head_shape_point as db_meg_ctf_head_shape_point
 from lib.db.base import Base
 from lib.db.decorators.string_path import StringPath
@@ -20,11 +23,21 @@ class DbMegCtfHeadShapeFile(Base):
     ID of the head shape file.
     """
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this head shape file, if any.
+    """
+
     path: Mapped[Path] = mapped_column('Path', StringPath)
     """
     Path of the head shape file relative to the LORIS data directory.
     """
 
+    insert_time: Mapped[datetime] = mapped_column('InsertTime', default=datetime.now)
+    """
+    The time at which this head shape file was created in LORIS.
+    """
+
     blake2b_hash: Mapped[str] = mapped_column('Blake2bHash')
     """
     Blake2B hash of the head shape file, which may be used to check that the on-disk file data
@@ -35,3 +48,8 @@ class DbMegCtfHeadShapeFile(Base):
     """
     3D points present in the head shape file.
     """
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this head shape file, if any.
+    """
diff --git a/python/lib/db/models/physio_event_file.py b/python/lib/db/models/physio_event_file.py
index cc7b4c602..ca82ddfd4 100644
--- a/python/lib/db/models/physio_event_file.py
+++ b/python/lib/db/models/physio_event_file.py
@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.imaging_file_type as db_imaging_file_type
 import lib.db.models.physio_event_parameter as db_physio_event_parameter
 import lib.db.models.physio_file as db_physio_file
@@ -24,8 +25,18 @@ class DbPhysioEventFile(Base):
     last_update    : Mapped[datetime]    = mapped_column('LastUpdate', default=datetime.now)
     last_written   : Mapped[datetime]    = mapped_column('LastWritten', default=datetime.now)
 
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this event file, if any.
+    """
+
     physio_file       : Mapped['db_physio_file.DbPhysioFile | None']                     = relationship('DbPhysioFile')
     project           : Mapped['db_project.DbProject | None']                            = relationship('DbProject')
     imaging_file_type : Mapped['db_imaging_file_type.DbImagingFileType | None']          = relationship('DbImagingFileType')
     task_events       : Mapped[list['db_physio_task_event.DbPhysioTaskEvent']]           = relationship('DbPhysioTaskEvent', back_populates='event_file')
     event_parameters  : Mapped[list['db_physio_event_parameter.DbPhysioEventParameter']] = relationship('DbPhysioEventParameter', back_populates='event_file')
+
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this event file, if any.
+    """
diff --git a/python/lib/db/models/physio_file.py b/python/lib/db/models/physio_file.py
index 03e014929..ac41e91d9 100644
--- a/python/lib/db/models/physio_file.py
+++ b/python/lib/db/models/physio_file.py
@@ -4,6 +4,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
+import lib.db.models.bids_file as db_bids_file
 import lib.db.models.meg_ctf_head_shape_file as db_meg_ctf_head_shape_file
 import lib.db.models.physio_channel as db_physio_channel
 import lib.db.models.physio_event_archive as db_physio_event_archive
@@ -33,7 +34,12 @@ class DbPhysioFile(Base):
     index            : Mapped[int | None]      = mapped_column('Index')
     parent_id        : Mapped[int | None]      = mapped_column('ParentID')
 
-    head_shape_file_id: Mapped[int | None] = mapped_column('HeadShapeFileID', ForeignKey('meg_ctf_head_shape_file.ID'))
+    bids_info_id: Mapped[int | None] = mapped_column('BidsInfoID', ForeignKey('bids_file.ID', ondelete='SET NULL'))
+    """
+    The ID of the BIDS information of this file, if any.
+    """
+
+    head_shape_file_id: Mapped[int | None] = mapped_column('HeadShapeFileID', ForeignKey('meg_ctf_head_shape_file.ID', ondelete='SET NULL'))
     """
     ID of the head shape file associated to this file, which is only present for MEG CTF files.
     """
@@ -48,6 +54,11 @@ class DbPhysioFile(Base):
     event_files   : Mapped[list['db_physio_event_file.DbPhysioEventFile']]         = relationship('DbPhysioEventFile', back_populates='physio_file')
     task_events   : Mapped[list['db_physio_task_event.DbPhysioTaskEvent']]         = relationship('DbPhysioTaskEvent', back_populates='physio_file')
 
+    bids_info: Mapped['db_bids_file.DbBidsFile | None'] = relationship('DbBidsFile')
+    """
+    The BIDS information of this file, if any.
+    """
+
     head_shape_file: Mapped['db_meg_ctf_head_shape_file.DbMegCtfHeadShapeFile | None'] = relationship('DbMegCtfHeadShapeFile')
     """
     The head shape file associated to this file, which is only present for MEG CTF files.
diff --git a/python/lib/db/queries/bids_dataset.py b/python/lib/db/queries/bids_dataset.py
new file mode 100644
index 000000000..72c0637ff
--- /dev/null
+++ b/python/lib/db/queries/bids_dataset.py
@@ -0,0 +1,16 @@
+from pathlib import Path
+
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.models.bids_dataset import DbBidsDataset
+
+
+def try_get_bids_dataset_with_path(db: Database, path: Path) -> DbBidsDataset | None:
+    """
+    Get a BIDS dataset from the database using its path, or return `None` if no dataset is found.
+    """
+
+    return db.execute(select(DbBidsDataset)
+        .where(DbBidsDataset.path == path)
+    ).scalar_one_or_none()
diff --git a/python/lib/db/queries/bids_file.py b/python/lib/db/queries/bids_file.py
new file mode 100644
index 000000000..3026c0175
--- /dev/null
+++ b/python/lib/db/queries/bids_file.py
@@ -0,0 +1,18 @@
+from pathlib import Path
+
+from sqlalchemy import select
+from sqlalchemy.orm import Session as Database
+
+from lib.db.models.bids_file import DbBidsFile
+
+
+def try_get_bids_file_with_dataset_id_path(db: Database, dataset_id: int, path: Path) -> DbBidsFile | None:
+    """
+    Get a BIDS file from the database using its dataset ID and path, or return `None` if no file is
+    found.
+    """
+
+    return db.execute(select(DbBidsFile)
+        .where(DbBidsFile.dataset_id == dataset_id)
+        .where(DbBidsFile.path == path)
+    ).scalar_one_or_none()
diff --git a/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py b/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py
index c9a4d75a4..3bcc7c59e 100644
--- a/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py
+++ b/python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py
@@ -676,6 +676,7 @@ def _register_into_files_and_parameter_file(self, nifti_rel_path):
             Path(nifti_rel_path),
             file_type,
             self.session,
+            None,
             self.scan_type,
             self.mri_scanner,
             self.dicom_archive,
diff --git a/python/lib/imaging_lib/file.py b/python/lib/imaging_lib/file.py
index ed754dd39..71628b702 100644
--- a/python/lib/imaging_lib/file.py
+++ b/python/lib/imaging_lib/file.py
@@ -2,6 +2,7 @@
 from datetime import date, datetime
 from pathlib import Path
 
+from lib.db.models.bids_file import DbBidsFile
 from lib.db.models.dicom_archive import DbDicomArchive
 from lib.db.models.file import DbFile
 from lib.db.models.imaging_file_type import DbImagingFileType
@@ -16,6 +17,7 @@ def register_mri_file(
     file_path: Path,
     file_type: DbImagingFileType,
     session: DbSession,
+    bids_info: DbBidsFile | None,
     scan_type: DbMriScanType | None,
     scanner: DbMriScanner | None,
     dicom_archive: DbDicomArchive | None,
@@ -46,6 +48,7 @@ def register_mri_file(
         echo_number              = echo_number,
         phase_encoding_direction = phase_encoding_direction,
         source_file_id           = None,
+        bids_info_id             = bids_info.id if bids_info is not None else None,
         scan_type_id             = scan_type.id if scan_type is not None else None,
         scanner_id               = scanner.id if scanner is not None else None,
         dicom_archive_id         = dicom_archive.id if dicom_archive is not None else None,
diff --git a/python/lib/physio/events.py b/python/lib/physio/events.py
index 6b4ee1cac..d560654d2 100644
--- a/python/lib/physio/events.py
+++ b/python/lib/physio/events.py
@@ -4,6 +4,7 @@
 from pathlib import Path
 from typing import Any
 
+from lib.db.models.bids_file import DbBidsFile
 from lib.db.models.physio_task_event_hed import DbPhysioTaskEventHed
 from lib.db.models.physio_task_event_opt import DbPhysioTaskEventOpt
 from lib.db.models.physio_task_event import DbPhysioTaskEvent
@@ -49,7 +50,12 @@ def from_file(physio_file: DbPhysioFile) -> 'EventDictFileSource':
         )
 
 
-def insert_event_dict_file(env: Env, source: EventDictFileSource, event_file_path: Path) -> DbPhysioEventFile:
+def insert_event_dict_file(
+    env: Env,
+    bids_info: DbBidsFile,
+    source: EventDictFileSource,
+    event_file_path: Path,
+) -> DbPhysioEventFile:
     """
     Insert an event dictionary file into the LORIS database.
     """
@@ -59,6 +65,7 @@ def insert_event_dict_file(env: Env, source: EventDictFileSource, event_file_pat
         project_id     = source.project.id,
         file_type      = 'json',
         file_path      = event_file_path,
+        bids_info_id   = bids_info.id,
     )
 
     env.db.add(event_dict_file)
@@ -202,7 +209,12 @@ def parse_and_insert_event_dict(
     return tag_dict
 
 
-def insert_events_file(env: Env, physio_file: DbPhysioFile, event_file_path: Path) -> DbPhysioEventFile:
+def insert_events_file(
+    env: Env,
+    physio_file: DbPhysioFile,
+    bids_info: DbBidsFile,
+    event_file_path: Path,
+) -> DbPhysioEventFile:
     """
     Insert an events file into the LORIS database.
     """
@@ -212,6 +224,7 @@ def insert_events_file(env: Env, physio_file: DbPhysioFile, event_file_path: Pat
         project_id     = physio_file.session.project.id,
         file_type      = 'tsv',
         file_path      = event_file_path,
+        bids_info_id   = bids_info.id,
     )
 
     env.db.add(event_dict_file)
diff --git a/python/lib/physio/file.py b/python/lib/physio/file.py
index e1891da3f..0042211b7 100644
--- a/python/lib/physio/file.py
+++ b/python/lib/physio/file.py
@@ -2,6 +2,7 @@
 from datetime import datetime
 from pathlib import Path
 
+from lib.db.models.bids_file import DbBidsFile
 from lib.db.models.imaging_file_type import DbImagingFileType
 from lib.db.models.physio_file import DbPhysioFile
 from lib.db.models.physio_modality import DbPhysioModality
@@ -18,6 +19,7 @@ def insert_physio_file(
     modality: DbPhysioModality,
     output_type: DbPhysioOutputType,
     acquisition_time: datetime | None,
+    bids_info: DbBidsFile | None,
 ) -> DbPhysioFile:
     """
     Insert a physiological file into the database.
@@ -31,6 +33,7 @@ def insert_physio_file(
         output_type_id   = output_type.id,
         acquisition_time = acquisition_time,
         inserted_by_user = getpass.getuser(),
+        bids_info_id     = bids_info.id if bids_info is not None else None,
     )
 
     env.db.add(file)
diff --git a/python/loris_bids_importer/src/loris_bids_importer/acquisitions.py b/python/loris_bids_importer/src/loris_bids_importer/acquisitions.py
index 41a663772..4d4f511e6 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/acquisitions.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/acquisitions.py
@@ -5,16 +5,16 @@
 from lib.logging import log, log_error
 from loris_bids_utils.info import BidsAcquisitionInfo
 
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.importer import BidsImporter
 
 T = TypeVar('T')
 
 
 def import_bids_acquisitions(
     env: Env,
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     acquisitions: list[tuple[T, BidsAcquisitionInfo]],
-    importer: Callable[[T, BidsAcquisitionInfo], None]
+    import_function: Callable[[T, BidsAcquisitionInfo], None]
 ):
     """
     Run an import function on a list of BIDS acquisitions, logging the overall import progress,
@@ -28,9 +28,9 @@ def import_bids_acquisitions(
         )
 
         try:
-            importer(acquisition, bids_info)
+            import_function(acquisition, bids_info)
             log(env, f"Successfully imported acquisition '{bids_info.name}'.")
-            import_env.imported_acquisitions_count += 1
+            importer.imported_acquisitions_count += 1
         except Exception as exception:
             log_error(
                 env,
@@ -40,4 +40,4 @@ def import_bids_acquisitions(
                     "Skipping."
                 )
             )
-            import_env.failed_acquisitions_count += 1
+            importer.failed_acquisitions_count += 1
diff --git a/python/loris_bids_importer/src/loris_bids_importer/args.py b/python/loris_bids_importer/src/loris_bids_importer/args.py
deleted file mode 100644
index b4d8f549d..000000000
--- a/python/loris_bids_importer/src/loris_bids_importer/args.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from dataclasses import dataclass
-from pathlib import Path
-from typing import Literal
-
-
-@dataclass
-class Args:
-    source_bids_path: Path
-    type: Literal[None, 'raw', 'derivative']
-    bids_validation: bool
-    create_candidate: bool
-    create_session: bool
-    copy: bool
-    verbose: bool
diff --git a/python/loris_bids_importer/src/loris_bids_importer/channels.py b/python/loris_bids_importer/src/loris_bids_importer/channels.py
index f75ce456a..e03593a6f 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/channels.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/channels.py
@@ -14,12 +14,13 @@
 from loris_utils.error import group_errors, group_errors_tuple
 
 from loris_bids_importer.copy_files import get_loris_bids_file_path
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.dataset import get_or_create_loris_bids_file
+from loris_bids_importer.importer import BidsImporter
 
 
 def insert_bids_channels_file(
     env: Env,
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     physio_file: DbPhysioFile,
     session: DbSession,
     acquisition: BidsAcquisitionInfo,
@@ -30,7 +31,7 @@ def insert_bids_channels_file(
     """
 
     loris_channels_file_path = get_loris_bids_file_path(
-        import_env, session, acquisition.data_type, channels_file.path
+        importer, session, acquisition.data_type, channels_file.path
     )
 
     blake2_hash = compute_file_blake2b_hash(channels_file.path)
@@ -48,6 +49,7 @@ def insert_bids_channels_file(
         ),
     )
 
+    get_or_create_loris_bids_file(env, importer, channels_file.path, loris_channels_file_path)
     insert_physio_file_parameter(env, physio_file, 'channel_file_blake2b_hash', blake2_hash)
 
     env.db.flush()
diff --git a/python/loris_bids_importer/src/loris_bids_importer/copy_files.py b/python/loris_bids_importer/src/loris_bids_importer/copy_files.py
index ac9f068b5..fda010ac9 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/copy_files.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/copy_files.py
@@ -2,50 +2,30 @@
 import shutil
 from pathlib import Path
 
-from lib.config import get_data_dir_path_config
 from lib.db.models.session import DbSession
 from lib.env import Env
-from loris_bids_utils.files.dataset_description import BidsDatasetDescriptionJsonFile
 from loris_bids_utils.files.participants import BidsParticipantsTsvFile
 from loris_bids_utils.files.scans import BidsScansTsvFile
 
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.dataset import get_or_create_loris_bids_file
+from loris_bids_importer.importer import BidsImporter
 
 
-def get_loris_bids_dataset_path(env: Env, dataset_description: BidsDatasetDescriptionJsonFile) -> Path:
-    """
-    Get the LORIS BIDS directory path for the BIDS dataset to import, and create that directory if
-    it does not exist yet.
-    """
-
-    # Sanitize the dataset metadata to have a usable name for the directory.
-    dataset_name    = re.sub(r'[^0-9a-zA-Z]+',   '_', dataset_description.data['Name'])
-    dataset_version = re.sub(r'[^0-9a-zA-Z\.]+', '_', dataset_description.data['BIDSVersion'])
-
-    data_dir_path = get_data_dir_path_config(env)
-    loris_bids_path = data_dir_path / 'bids_imports' / f'{dataset_name}_BIDSVersion_{dataset_version}'
-
-    if not loris_bids_path.exists():
-        loris_bids_path.mkdir()
-
-    return loris_bids_path
-
-
-def get_loris_bids_root_file_path(import_env: BidsImportEnv, file_path: Path) -> Path:
+def get_loris_bids_root_file_path(importer: BidsImporter, file_path: Path) -> Path:
     """
     Get the path of a BIDS file relative to the LORIS data directory, maintaining the same relative
     path in the LORIS BIDS dataset as within the source BIDS dataset.
     """
 
     # In the import is run in no-copy mode, return the original file path.
-    if import_env.loris_bids_path is None:
-        return file_path.relative_to(import_env.data_dir_path)
+    if not importer.args.copy:
+        return file_path.relative_to(importer.data_dir_path)
 
-    return import_env.loris_bids_path / file_path.relative_to(import_env.source_bids_path)
+    return importer.loris_bids_dataset.path / file_path.relative_to(importer.args.source_bids_path)
 
 
 def get_loris_bids_file_path(
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     session: DbSession,
     data_type: str,
     file_path: Path,
@@ -56,20 +36,20 @@ def get_loris_bids_file_path(
     """
 
     # In the import is run in no-copy mode, return the original file path.
-    if import_env.loris_bids_path is None:
-        return file_path.relative_to(import_env.data_dir_path)
+    if not importer.args.copy:
+        return file_path.relative_to(importer.data_dir_path)
 
     # If the file is a derivative, the path is unpredictable, so return a copy of that path in the
     # LORIS BIDS dataset.
     if derivative:
-        return import_env.loris_bids_path / file_path.relative_to(import_env.source_bids_path)
+        return importer.loris_bids_dataset.path / file_path.relative_to(importer.args.source_bids_path)
 
     # Otherwise, normalize the subject and session directory names using the LORIS session
     # information.
     loris_file_name = get_loris_bids_file_name(file_path.name, session)
 
     return (
-        import_env.loris_bids_path
+        importer.loris_bids_dataset.path
         / f'sub-{session.candidate.psc_id}'
         / f'ses-{session.visit_label}'
         / data_type
@@ -91,34 +71,34 @@ def get_loris_bids_file_name(file_name: str, session: DbSession) -> str:
     return f'sub-{session.candidate.psc_id}_ses-{session.visit_label}_{file_name}'
 
 
-def get_loris_scans_path(import_env: BidsImportEnv, scans_file: BidsScansTsvFile, session: DbSession) -> Path:
+def get_loris_scans_path(importer: BidsImporter, scans_file: BidsScansTsvFile, session: DbSession) -> Path:
     """
     Get the path of a `scans.tsv` file in LORIS, relative to the LORIS data directory.
     """
 
     # In the import is run in no-copy mode, return the original file path.
-    if import_env.loris_bids_path is None:
-        return scans_file.path.relative_to(import_env.data_dir_path)
+    if not importer.args.copy:
+        return scans_file.path.relative_to(importer.data_dir_path)
 
     loris_file_name = get_loris_bids_file_name(scans_file.path.name, session)
     return (
-        import_env.loris_bids_path
+        importer.loris_bids_dataset.path
         / f'sub-{session.candidate.psc_id}'
         / f'ses-{session.visit_label}'
         / loris_file_name
     )
 
 
-def copy_loris_bids_file(import_env: BidsImportEnv, file_path: Path, loris_file_path: Path):
+def copy_loris_bids_file(importer: BidsImporter, file_path: Path, loris_file_path: Path):
     """
     Copy a BIDS file to the LORIS data directory, unless the no-copy mode is enabled.
     """
 
     # Do not copy the file in no-copy mode.
-    if import_env.loris_bids_path is None:
+    if not importer.args.copy:
         return
 
-    full_loris_file_path = import_env.data_dir_path / loris_file_path
+    full_loris_file_path = importer.data_dir_path / loris_file_path
 
     if full_loris_file_path.exists():
         raise Exception(f"File '{loris_file_path}' already exists in the LORIS data directory.")
@@ -130,31 +110,29 @@ def copy_loris_bids_file(import_env: BidsImportEnv, file_path: Path, loris_file_
         shutil.copytree(file_path, full_loris_file_path)
 
 
-def copy_bids_static_files(import_env: BidsImportEnv):
+def copy_bids_static_files(env: Env, importer: BidsImporter):
     """
     Copy the static files of the source BIDS dataset to the LORIS BIDS dataset.
     """
 
-    # Do not copy files in no-copy mode.
-    if import_env.loris_bids_path is None:
-        return
-
     for file_name in ['README', 'dataset_description.json']:
-        source_file_path = import_env.source_bids_path / file_name
+        source_file_path = importer.args.source_bids_path / file_name
         if not source_file_path.is_file():
             continue
 
-        loris_file_path = import_env.loris_bids_path / file_name
+        loris_file_path = importer.loris_bids_dataset.path / file_name
 
         # Do not copy the file if it is already present during an incremental import.
-        if (import_env.data_dir_path / loris_file_path).is_file():
+        if (importer.data_dir_path / loris_file_path).is_file():
             continue
 
-        copy_loris_bids_file(import_env, source_file_path, loris_file_path)
+        get_or_create_loris_bids_file(env, importer, source_file_path, loris_file_path)
+        copy_loris_bids_file(importer, source_file_path, loris_file_path)
 
 
 def copy_bids_participants_file(
-    import_env: BidsImportEnv,
+    env: Env,
+    importer: BidsImporter,
     participants_file: BidsParticipantsTsvFile,
     loris_participants_path: Path,
 ):
@@ -163,11 +141,13 @@ def copy_bids_participants_file(
     necessary.
     """
 
+    get_or_create_loris_bids_file(env, importer, participants_file.path, loris_participants_path)
+
     # Do not copy the file in no-copy mode.
-    if import_env.loris_bids_path is None:
+    if not importer.args.copy:
         return
 
-    participants_path = import_env.data_dir_path / loris_participants_path
+    participants_path = importer.data_dir_path / loris_participants_path
     if participants_path.exists():
         participants_file.merge(BidsParticipantsTsvFile(participants_path))
 
@@ -175,16 +155,18 @@ def copy_bids_participants_file(
     participants_file.write(participants_path)
 
 
-def copy_bids_scans_file(import_env: BidsImportEnv, scans_file: BidsScansTsvFile, loris_scans_path: Path):
+def copy_bids_scans_file(env: Env, importer: BidsImporter, scans_file: BidsScansTsvFile, loris_scans_path: Path):
     """
     Copy some `scans.tsv` rows into a LORIS `scans.tsv` file, creating it if necessary.
     """
 
+    get_or_create_loris_bids_file(env, importer, scans_file.path, loris_scans_path)
+
     # Do not copy the file in no-copy mode.
-    if import_env.loris_bids_path is None:
+    if not importer.args.copy:
         return
 
-    scans_path = import_env.data_dir_path / loris_scans_path
+    scans_path = importer.data_dir_path / loris_scans_path
     if scans_path.exists():
         scans_file.merge(BidsScansTsvFile(scans_path))
 
diff --git a/python/loris_bids_importer/src/loris_bids_importer/dataset.py b/python/loris_bids_importer/src/loris_bids_importer/dataset.py
new file mode 100644
index 000000000..9419cb5ab
--- /dev/null
+++ b/python/loris_bids_importer/src/loris_bids_importer/dataset.py
@@ -0,0 +1,142 @@
+import re
+from datetime import datetime
+from pathlib import Path
+
+from lib.config import get_data_dir_path_config
+from lib.db.models.bids_dataset import DbBidsDataset
+from lib.db.models.bids_file import DbBidsFile
+from lib.db.queries.bids_dataset import try_get_bids_dataset_with_path
+from lib.db.queries.bids_file import try_get_bids_file_with_dataset_id_path
+from lib.env import Env
+from lib.logging import log_error_exit
+from loris_bids_utils.reader import BidsDatasetReader
+from loris_utils.crypto import compute_file_blake2b_hash
+
+from loris_bids_importer.importer import BidsImporter, BidsImporterArgs
+
+
+def make_bids_importer(env: Env, args: BidsImporterArgs, bids: BidsDatasetReader) -> BidsImporter:
+    """
+    Make the LORIS BIDS importer object from the BIDS import input information.
+    """
+
+    data_dir_path = get_data_dir_path_config(env)
+
+    if args.copy:
+        loris_bids_path = get_copy_dataset_path(env, bids, data_dir_path)
+    else:
+        loris_bids_path = get_no_copy_dataset_path(env, bids, data_dir_path)
+
+    loris_bids_dataset = get_or_create_loris_bids_dataset(env, loris_bids_path)
+
+    return BidsImporter(
+        args               = args,
+        data_dir_path      = data_dir_path,
+        loris_bids_dataset = loris_bids_dataset
+    )
+
+
+def get_copy_dataset_path(env: Env, bids: BidsDatasetReader, data_dir_path: Path) -> Path:
+    """
+    Get the LORIS BIDS dataset path relative to the LORIS data directory in the copy mode, creating
+    it if it does not exist yet.
+    """
+
+    try:
+        dataset_description = bids.dataset_description_file
+    except Exception as error:
+        log_error_exit(env, str(error))
+
+    if dataset_description is None:
+        log_error_exit(
+            env,
+            "No file 'dataset_description.json' found in the input BIDS dataset.",
+        )
+
+    # Sanitize the dataset metadata to have a usable name for the directory.
+    dataset_name    = re.sub(r'[^0-9a-zA-Z]+',   '_', dataset_description.data['Name'])
+    dataset_version = re.sub(r'[^0-9a-zA-Z\.]+', '_', dataset_description.data['BIDSVersion'])
+
+    loris_bids_path = Path('bids_imports') / f'{dataset_name}_BIDSVersion_{dataset_version}'
+
+    # Create the BIDS dataset directory if it does not exist yet.
+    (data_dir_path / loris_bids_path).mkdir(exist_ok=True)
+
+    return loris_bids_path
+
+
+def get_no_copy_dataset_path(env: Env, bids: BidsDatasetReader, data_dir_path: Path) -> Path:
+    """
+    Get the LORIS BIDS dataset path relative to the LORIS data directory in the no-copy mode.
+    """
+
+    if not bids.path.is_relative_to(data_dir_path):
+        log_error_exit(
+            env,
+            "The source BIDS dataset should be inside the LORIS data directory in no-copy mode.",
+        )
+
+    return bids.path.relative_to(data_dir_path)
+
+
+def get_or_create_loris_bids_dataset(env: Env, bids_path: Path) -> DbBidsDataset:
+    """
+    Get a BIDS dataset from the database using its LORIS data-directory-relative path,
+    or create it if it does not already exist.
+    """
+
+    bids_dataset = try_get_bids_dataset_with_path(env.db, bids_path)
+    if bids_dataset is not None:
+        return bids_dataset
+
+    bids_dataset = DbBidsDataset(
+        path        = bids_path,
+        insert_time = datetime.now(),
+    )
+
+    env.db.add(bids_dataset)
+    env.db.flush()
+
+    return bids_dataset
+
+
+def get_or_create_loris_bids_file(
+    env: Env,
+    importer: BidsImporter,
+    source_file_path: Path,
+    loris_file_path: Path,
+) -> DbBidsFile:
+    """
+    Create or update the LORIS database record for a BIDS file.
+    """
+
+    # The LORIS file path is relative to the LORIS data directory, it needs to be made relative to
+    # its LORIS BIDS dataset instead.
+    bids_file_path = loris_file_path.relative_to(importer.loris_bids_dataset.path)
+
+    source_bids_file_path = source_file_path.relative_to(importer.args.source_bids_path)
+
+    derivative = source_bids_file_path.parts[0] == 'derivatives'
+
+    blake2b_hash = compute_file_blake2b_hash(source_file_path)
+
+    bids_file = try_get_bids_file_with_dataset_id_path(env.db, importer.loris_bids_dataset.id, bids_file_path)
+
+    if bids_file is None:
+        bids_file = DbBidsFile(
+            dataset_id    = importer.loris_bids_dataset.id,
+            path          = bids_file_path,
+            source_path   = source_bids_file_path,
+            insert_time   = datetime.now(),
+            blake2b_hash  = blake2b_hash,
+            derivative    = derivative,
+        )
+
+        env.db.add(bids_file)
+    else:
+        bids_file.source_path = source_bids_file_path
+        bids_file.blake2b_hash = blake2b_hash
+
+    env.db.flush()
+
+    return bids_file
diff --git a/python/loris_bids_importer/src/loris_bids_importer/eeg/main.py b/python/loris_bids_importer/src/loris_bids_importer/eeg/main.py
index 0ea7714fe..0a35b3161 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/eeg/main.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/eeg/main.py
@@ -29,10 +29,11 @@
 from loris_bids_importer.archive import import_physio_event_archive, import_physio_file_archive
 from loris_bids_importer.channels import insert_bids_channels_file
 from loris_bids_importer.copy_files import copy_loris_bids_file, get_loris_bids_file_path, get_loris_scans_path
+from loris_bids_importer.dataset import get_or_create_loris_bids_file
 from loris_bids_importer.eeg.physiological import Physiological
-from loris_bids_importer.env import BidsImportEnv
 from loris_bids_importer.events import insert_bids_event_dict_file, insert_bids_events_file
 from loris_bids_importer.file_type import get_check_bids_imaging_file_type_from_extension
+from loris_bids_importer.importer import BidsImporter
 from loris_bids_importer.physio import (
     get_check_bids_physio_file_hash,
     get_check_bids_physio_modality,
@@ -46,8 +47,8 @@ class Eeg:
     into the database by calling the loris_bids_importer.eeg.physiological class.
     """
 
-    def __init__(self, env: Env, import_env: BidsImportEnv, bids_layout, bids_info: BidsDataTypeInfo,
-                 session: DbSession, db, dataset_tag_dict, dataset_type):
+    def __init__(self, env: Env, importer: BidsImporter, bids_layout, bids_info: BidsDataTypeInfo,
+                 session: DbSession, db, dataset_tag_dict):
         """
         Constructor method for the Eeg class.
 
@@ -60,8 +61,6 @@ def __init__(self, env: Env, import_env: BidsImportEnv, bids_layout, bids_info:
         :param info         : The BIDS import pipeline information
         :param dataset_tag_dict      : Dict of dataset-inherited HED tags
          :type dataset_tag_dict      : dict
-        :param dataset_type          : raw | derivative. Type of the dataset
-         :type dataset_type          : string
         """
 
         self.env = env
@@ -71,14 +70,14 @@ def __init__(self, env: Env, import_env: BidsImportEnv, bids_layout, bids_info:
 
         # load the LORIS BIDS import root directory where the eeg files will
         # be copied
-        self.info                = import_env
-        self.data_dir            = self.info.data_dir_path
+        self.importer = importer
+        self.data_dir = self.importer.data_dir_path
 
         # load bids subject, visit and modality
         self.bids_info = bids_info
 
         # load dataset tag dict. Used to ensure HED tags aren't duplicated
-        self.dataset_tag_dict   = dataset_tag_dict
+        self.dataset_tag_dict = dataset_tag_dict
 
         # load database handler object
         self.db = db
@@ -99,13 +98,14 @@ def __init__(self, env: Env, import_env: BidsImportEnv, bids_layout, bids_info:
             self.scans_file = BidsScansTsvFile(Path(scans_file_path))
 
         # register the data into LORIS
-        if (dataset_type and dataset_type == 'raw'):
-            self.register_data(detect=False)
-        elif (dataset_type and dataset_type == 'derivative'):
-            self.register_data(derivatives=True, detect=False)
-        else:
-            self.register_data()
-            self.register_data(derivatives=True)
+        match importer.args.type:
+            case 'raw':
+                self.register_data(detect=False)
+            case 'derivative':
+                self.register_data(derivatives=True, detect=False)
+            case None:
+                self.register_data()
+                self.register_data(derivatives=True)
 
         env.db.commit()
 
@@ -216,7 +216,7 @@ def register_data(self, derivatives=False, detect=True):
             if get_ephys_visualization_enabled_config(self.env):
                 create_physio_channels_chunks(self.env, eeg_file)
 
-            self.info.imported_acquisitions_count += 1
+            self.importer.imported_acquisitions_count += 1
 
     def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
         """
@@ -288,6 +288,7 @@ def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
                 eeg_file_data = sidecar_json.data
 
                 sidecar_json_path = self.copy_file_to_loris_bids_dir(sidecar_json.path, derivatives)
+                get_or_create_loris_bids_file(self.env, self.importer, sidecar_json.path, sidecar_json_path)
                 eeg_file_data['eegjson_file'] = str(sidecar_json_path)
 
                 json_blake2 = compute_file_blake2b_hash(sidecar_json.path)
@@ -313,7 +314,7 @@ def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
                         print(f"ERROR: {error}")
                         sys.exit(lib.exitcode.PROGRAM_EXECUTION_FAILURE)
 
-                    loris_scans_path = get_loris_scans_path(self.info, self.scans_file, self.session)
+                    loris_scans_path = get_loris_scans_path(self.importer, self.scans_file, self.session)
                     eeg_file_data['scans_tsv_file'] = loris_scans_path
                     scans_blake2 = compute_file_blake2b_hash(self.scans_file.path)
                     eeg_file_data['physiological_scans_tsv_file_bake2hash'] = scans_blake2
@@ -346,6 +347,13 @@ def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
                 eeg_file.path, derivatives
             )
 
+            bids_info = get_or_create_loris_bids_file(
+                self.env,
+                self.importer,
+                eeg_file_path,
+                eeg_path,
+            )
+
             # insert the file along with its information into
             # physiological_file and physiological_parameter_file tables
             physio_file = insert_physio_file(
@@ -355,13 +363,14 @@ def fetch_and_insert_eeg_files(self, derivatives=False, detect=True):
                 file_type,
                 modality,
                 output_type,
-                eeg_acq_time
+                eeg_acq_time,
+                bids_info,
             )
 
             insert_physio_file_parameters(self.env, physio_file, eeg_file_data)
             self.env.db.commit()
 
-            if self.info.loris_bids_path:
+            if self.importer.args.copy:
                 # If we copy the file in assembly_bids and
                 # if the EEG file was a set file, then update the filename for the .set
                 # and .fdt files in the .set file so it can find the proper file for
@@ -437,6 +446,7 @@ def fetch_and_insert_electrode_file(
                     # get the blake2b hash of the electrode file
                     blake2 = compute_file_blake2b_hash(electrode_file.path)
 
+                    get_or_create_loris_bids_file(self.env, self.importer, Path(electrode_file.path), electrode_path)
                     # insert the electrode data in the database
                     electrode_ids = physiological.insert_electrode_file(
                         electrode_data, electrode_path, physiological_file, blake2
@@ -477,6 +487,14 @@ def fetch_and_insert_electrode_file(
                             electrode_metadata = json.load(metadata_file)
                         # get the blake2b hash of the json events file
                         blake2 = compute_file_blake2b_hash(coordsystem_metadata_file.path)
+
+                        get_or_create_loris_bids_file(
+                            self.env,
+                            self.importer,
+                            Path(coordsystem_metadata_file.path),
+                            electrode_metadata_path,
+                        )
+
                         # insert event metadata in the database
                         physiological.insert_electrode_metadata(
                             electrode_metadata,
@@ -533,7 +551,7 @@ def fetch_and_insert_channel_file(
         # Insert the channel data in the database.
         return insert_bids_channels_file(
             self.env,
-            self.info,
+            self.importer,
             physiological_file,
             self.session,
             self.bids_info,
@@ -611,6 +629,7 @@ def fetch_and_insert_event_files(
 
                     _, file_tag_dict = insert_bids_event_dict_file(
                         self.env,
+                        self.importer,
                         EventDictFileSource.from_file(physiological_file),
                         event_dict_file,
                         event_metadata_path,
@@ -628,6 +647,7 @@ def fetch_and_insert_event_files(
             # insert event data in the database
             insert_bids_events_file(
                 self.env,
+                self.importer,
                 physiological_file,
                 events_data_file,
                 event_path,
@@ -658,7 +678,7 @@ def copy_file_to_loris_bids_dir(self, file, derivatives=False):
         """
 
         loris_file_path = get_loris_bids_file_path(
-            self.info,
+            self.importer,
             self.session,
             self.bids_info.data_type,
             Path(file),
@@ -669,7 +689,7 @@ def copy_file_to_loris_bids_dir(self, file, derivatives=False):
         # the same metadata file several times if it is shared acquisitions. A warning has been
         # added.
         # TODO: Properly handle metadata files shared across several acquisitions.
-        full_file_path = self.info.data_dir_path / loris_file_path
+        full_file_path = self.importer.data_dir_path / loris_file_path
         if full_file_path.exists():
             log_warning(
                 self.env,
@@ -678,5 +698,5 @@ def copy_file_to_loris_bids_dir(self, file, derivatives=False):
 
             return loris_file_path
 
-        copy_loris_bids_file(self.info, Path(file), loris_file_path)
+        copy_loris_bids_file(self.importer, Path(file), loris_file_path)
         return loris_file_path
diff --git a/python/loris_bids_importer/src/loris_bids_importer/events.py b/python/loris_bids_importer/src/loris_bids_importer/events.py
index a3e962ba8..c806ee604 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/events.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/events.py
@@ -24,12 +24,13 @@
 from loris_utils.crypto import compute_file_blake2b_hash
 
 from loris_bids_importer.copy_files import copy_loris_bids_file, get_loris_bids_root_file_path
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.dataset import get_or_create_loris_bids_file
+from loris_bids_importer.importer import BidsImporter
 
 
 def import_bids_root_event_dict_file(
     env: Env,
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     project: DbProject,
     bids_event_dict_file: BidsJsonFile,
 ) -> tuple[DbPhysioEventFile, dict[str, dict[str, list[list[TagGroupMember]]]]]:
@@ -37,12 +38,13 @@ def import_bids_root_event_dict_file(
     Import a root-level BIDS event dictionary file and its associated HED tags into LORIS.
     """
 
-    loris_event_dict_file_path = get_loris_bids_root_file_path(import_env, bids_event_dict_file.path)
+    loris_event_dict_file_path = get_loris_bids_root_file_path(importer, bids_event_dict_file.path)
 
-    copy_loris_bids_file(import_env, bids_event_dict_file.path, loris_event_dict_file_path)
+    copy_loris_bids_file(importer, bids_event_dict_file.path, loris_event_dict_file_path)
 
     event_dict_file, hed_tags_dict = insert_bids_event_dict_file(
         env,
+        importer,
         EventDictFileSource.from_dataset(project),
         bids_event_dict_file,
         loris_event_dict_file_path,
@@ -55,6 +57,7 @@ def import_bids_root_event_dict_file(
 
 def insert_bids_event_dict_file(
     env: Env,
+    importer: BidsImporter,
     source: EventDictFileSource,
     bids_event_dict_file: BidsJsonFile,
     loris_event_dict_file_path: Path,
@@ -63,7 +66,8 @@ def insert_bids_event_dict_file(
     Insert a BIDS event dictionary file and its associated HED tags into the LORIS database.
     """
 
-    event_dict_file = insert_event_dict_file(env, source, loris_event_dict_file_path)
+    bids_info = get_or_create_loris_bids_file(env, importer, bids_event_dict_file.path, loris_event_dict_file_path)
+    event_dict_file = insert_event_dict_file(env, bids_info, source, loris_event_dict_file_path)
 
     blake2b_hash = compute_file_blake2b_hash(bids_event_dict_file.path)
 
@@ -80,6 +84,7 @@ def insert_bids_event_dict_file(
 # TODO: This function contains a lot of legacy code and needs to be refactored.
 def insert_bids_events_file(
     env: Env,
+    importer: BidsImporter,
     physio_file: DbPhysioFile,
     events_file: BidsEventsTsvFile,
     loris_events_file_path: Path,
@@ -99,7 +104,8 @@ def insert_bids_events_file(
 
     blake2_hash = compute_file_blake2b_hash(events_file.path)
 
-    event_file = insert_events_file(env, physio_file, loris_events_file_path)
+    bids_info = get_or_create_loris_bids_file(env, importer, events_file.path, loris_events_file_path)
+    event_file = insert_events_file(env, physio_file, bids_info, loris_events_file_path)
 
     # insert blake2b hash of task event file into physiological_parameter_file
     insert_physio_file_parameter(env, physio_file, 'event_file_blake2b_hash', blake2_hash)
diff --git a/python/loris_bids_importer/src/loris_bids_importer/env.py b/python/loris_bids_importer/src/loris_bids_importer/importer.py
similarity index 58%
rename from python/loris_bids_importer/src/loris_bids_importer/env.py
rename to python/loris_bids_importer/src/loris_bids_importer/importer.py
index d1b074e80..efa44f373 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/env.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/importer.py
@@ -1,26 +1,44 @@
 from dataclasses import dataclass
 from pathlib import Path
+from typing import Literal
+
+from lib.db.models.bids_dataset import DbBidsDataset
 
 
 @dataclass
-class BidsImportEnv:
+class BidsImporterArgs:
     """
-    Information about a specific BIDS import pipeline run.
+    The CLI arguments given to the BIDS importer.
     """
 
-    data_dir_path: Path
+    source_bids_path: Path
+    type: Literal['raw', 'derivative', None]
+    bids_validation: bool
+    create_candidate: bool
+    create_session: bool
+    copy: bool
+    verbose: bool
+
+
+@dataclass
+class BidsImporter:
     """
-    The LORIS data directory path.
+    Information about the current BIDS import pipeline run.
     """
 
-    source_bids_path: Path
+    args: BidsImporterArgs
+    """
+    The CLI arguments given to the BIDS importer.
+    """
+
+    data_dir_path: Path
     """
-    The source BIDS directory path.
+    The LORIS data directory path.
     """
 
-    loris_bids_path: Path | None
+    loris_bids_dataset: DbBidsDataset
     """
-    The LORIS BIDS directory path for this import, relative to the LORIS data directory.
+    The LORIS BIDS dataset populated by this import.
     """
 
     imported_acquisitions_count: int = 0
diff --git a/python/loris_bids_importer/src/loris_bids_importer/main.py b/python/loris_bids_importer/src/loris_bids_importer/main.py
index 538011ac2..1f350c051 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/main.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/main.py
@@ -1,6 +1,6 @@
 from typing import Any
 
-from lib.config import get_data_dir_path_config, get_default_bids_visit_label_config
+from lib.config import get_default_bids_visit_label_config
 from lib.database import Database
 from lib.db.models.session import DbSession
 from lib.db.queries.candidate import try_get_candidate_with_psc_id
@@ -10,31 +10,28 @@
 from loris_bids_utils.mri.reader import BidsMriDataTypeReader
 from loris_bids_utils.reader import BidsDatasetReader, BidsDataTypeReader, BidsSessionReader
 
-from loris_bids_importer.args import Args
 from loris_bids_importer.copy_files import (
     copy_bids_participants_file,
     copy_bids_scans_file,
     copy_bids_static_files,
-    get_loris_bids_dataset_path,
     get_loris_bids_root_file_path,
     get_loris_scans_path,
 )
+from loris_bids_importer.dataset import make_bids_importer
 from loris_bids_importer.eeg.main import Eeg
-from loris_bids_importer.env import BidsImportEnv
 from loris_bids_importer.events import import_bids_root_event_dict_file
+from loris_bids_importer.importer import BidsImporter, BidsImporterArgs
 from loris_bids_importer.mri.main import import_bids_mri_data_type
 from loris_bids_importer.print import print_bids_import_summary, print_bids_info
 from loris_bids_importer.validation.sessions import validate_bids_sessions
 from loris_bids_importer.validation.subjects import validate_bids_subjects
 
 
-def import_bids_dataset(env: Env, args: Args, legacy_db: Database):
+def import_bids_dataset(env: Env, args: BidsImporterArgs, legacy_db: Database):
     """
     Read the provided BIDS dataset and import it into LORIS.
     """
 
-    data_dir_path = get_data_dir_path_config(env)
-
     log(env, "Parsing BIDS dataset...")
 
     bids = BidsDatasetReader(args.source_bids_path, args.type == 'derivative', args.bids_validation)
@@ -61,33 +58,11 @@ def import_bids_dataset(env: Env, args: Args, legacy_db: Database):
 
     env.db.commit()
 
-    # Get the LORIS BIDS import directory path and create the directory if needed.
-
-    if args.copy:
-        try:
-            dataset_description = bids.dataset_description_file
-        except Exception as error:
-            log_error_exit(env, str(error))
-
-        if dataset_description is None:
-            log_error_exit(
-                env,
-                "No file 'dataset_description.json' found in the input BIDS dataset.",
-            )
-
-        loris_bids_path = get_loris_bids_dataset_path(env, dataset_description)
-    else:
-        loris_bids_path = None
-
-    import_env = BidsImportEnv(
-        data_dir_path     = data_dir_path,
-        loris_bids_path   = loris_bids_path.relative_to(data_dir_path) if loris_bids_path is not None else None,
-        source_bids_path  = args.source_bids_path,
-    )
+    importer = make_bids_importer(env, args, bids)
 
     # Copy the static BIDS files.
 
-    copy_bids_static_files(import_env)
+    copy_bids_static_files(env, importer)
 
     # Get the BIDS event dictionary.
 
@@ -97,7 +72,7 @@ def import_bids_dataset(env: Env, args: Args, legacy_db: Database):
     else:
         _, dataset_tag_dict = import_bids_root_event_dict_file(
             env,
-            import_env,
+            importer,
             single_project,
             bids.event_dict_file,
         )
@@ -105,23 +80,22 @@ def import_bids_dataset(env: Env, args: Args, legacy_db: Database):
     # Copy the `participants.tsv` file rows.
 
     if bids.participants_file is not None:
-        loris_participants_path = get_loris_bids_root_file_path(import_env, bids.participants_file.path)
-        copy_bids_participants_file(import_env, bids.participants_file, loris_participants_path)
+        loris_participants_path = get_loris_bids_root_file_path(importer, bids.participants_file.path)
+        copy_bids_participants_file(env, importer, bids.participants_file, loris_participants_path)
 
     # Process each session directory.
 
     for bids_session in bids.sessions:
-        import_bids_session(env, import_env, args, bids_session, dataset_tag_dict, legacy_db)
+        import_bids_session(env, importer, bids_session, dataset_tag_dict, legacy_db)
 
     # Print import summary.
 
-    print_bids_import_summary(env, import_env)
+    print_bids_import_summary(env, importer)
 
 
 def import_bids_session(
     env: Env,
-    import_env: BidsImportEnv,
-    args: Args,
+    importer: BidsImporter,
     bids_session: BidsSessionReader,
     dataset_tag_dict: dict[Any, Any],
     legacy_db: Database,
@@ -155,8 +129,8 @@ def import_bids_session(
     try:
         # Read the scans.tsv property to raise an exception if the file is incorrect.
         if bids_session.scans_file is not None:
-            loris_scans_path = get_loris_scans_path(import_env, bids_session.scans_file, session)
-            copy_bids_scans_file(import_env, bids_session.scans_file, loris_scans_path)
+            loris_scans_path = get_loris_scans_path(importer, bids_session.scans_file, session)
+            copy_bids_scans_file(env, importer, bids_session.scans_file, loris_scans_path)
     except Exception as exception:
         log_warning(
             env,
@@ -166,13 +140,12 @@ def import_bids_session(
     # Process each data type directory.
 
     for data_type in bids_session.data_types:
-        import_bids_data_type(env, import_env, args, session, data_type, dataset_tag_dict, legacy_db)
+        import_bids_data_type(env, importer, session, data_type, dataset_tag_dict, legacy_db)
 
 
 def import_bids_data_type(
     env: Env,
-    import_env: BidsImportEnv,
-    args: Args,
+    importer: BidsImporter,
     session: DbSession,
     data_type: BidsDataTypeReader,
     dataset_tag_dict: dict[Any, Any],
@@ -189,15 +162,14 @@ def import_bids_data_type(
 
     match data_type:
         case BidsMriDataTypeReader():
-            import_bids_mri_data_type(env, import_env, session, data_type)
+            import_bids_mri_data_type(env, importer, session, data_type)
         case BidsDataTypeReader():
-            import_bids_eeg_data_type_files(env, import_env, args, session, data_type, dataset_tag_dict, legacy_db)
+            import_bids_eeg_data_type_files(env, importer, session, data_type, dataset_tag_dict, legacy_db)
 
 
 def import_bids_eeg_data_type_files(
     env: Env,
-    import_env: BidsImportEnv,
-    args: Args,
+    importer: BidsImporter,
     session: DbSession,
     data_type: BidsDataTypeReader,
     dataset_tag_dict: dict[Any, Any],
@@ -210,13 +182,12 @@ def import_bids_eeg_data_type_files(
     try:
         Eeg(
             env              = env,
-            import_env       = import_env,
+            importer         = importer,
             bids_layout      = data_type.session.subject.dataset.layout,
             bids_info        = data_type.info,
             db               = legacy_db,
             session          = session,
             dataset_tag_dict = dataset_tag_dict,
-            dataset_type     = args.type,
         )
     except Exception as exception:
         log_error(
@@ -227,4 +198,4 @@ def import_bids_eeg_data_type_files(
                 "Skipping."
             )
         )
-        import_env.failed_acquisitions_count += 1
+        importer.failed_acquisitions_count += 1
diff --git a/python/loris_bids_importer/src/loris_bids_importer/mri/main.py b/python/loris_bids_importer/src/loris_bids_importer/mri/main.py
index 829b6988a..2e246c5a8 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/mri/main.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/mri/main.py
@@ -20,8 +20,9 @@
 
 from loris_bids_importer.acquisitions import import_bids_acquisitions
 from loris_bids_importer.copy_files import copy_loris_bids_file, get_loris_bids_file_path
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.dataset import get_or_create_loris_bids_file
 from loris_bids_importer.file_type import get_check_bids_imaging_file_type_from_extension
+from loris_bids_importer.importer import BidsImporter
 from loris_bids_importer.mri.sidecar import add_bids_mri_sidecar_file_parameters
 from loris_bids_importer.scans import add_bids_scans_file_parameters
 
@@ -44,7 +45,7 @@
 
 def import_bids_mri_data_type(
     env: Env,
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     session: DbSession,
     data_type: BidsMriDataTypeReader,
 ):
@@ -54,11 +55,11 @@ def import_bids_mri_data_type(
 
     import_bids_acquisitions(
         env,
-        import_env,
+        importer,
         data_type.acquisitions,
         lambda acquisition, bids_info: import_bids_mri_acquisition(
             env,
-            import_env,
+            importer,
             session,
             acquisition,
             bids_info,
@@ -68,7 +69,7 @@ def import_bids_mri_data_type(
 
 def import_bids_mri_acquisition(
     env: Env,
-    import_env: BidsImportEnv,
+    importer: BidsImporter,
     session: DbSession,
     acquisition: MriAcquisition,
     bids_info: BidsAcquisitionInfo,
@@ -80,14 +81,14 @@ def import_bids_mri_acquisition(
     # The files to copy to LORIS, with the source path on the left and the LORIS path on the right.
     files_to_copy: list[tuple[Path, Path]] = []
 
-    loris_file_path = get_loris_bids_file_path(import_env, session, bids_info.data_type, acquisition.nifti_path)
+    loris_file_path = get_loris_bids_file_path(importer, session, bids_info.data_type, acquisition.nifti_path)
     files_to_copy.append((acquisition.nifti_path, loris_file_path))
 
     # Check whether the file is already registered in LORIS.
 
     loris_file = try_get_file_with_path(env.db, loris_file_path)
     if loris_file is not None:
-        import_env.ignored_acquisitions_count += 1
+        importer.ignored_acquisitions_count += 1
         log(env, f"File '{loris_file_path}' is already registered in LORIS. Skipping.")
         return
 
@@ -125,7 +126,7 @@ def import_bids_mri_acquisition(
     if acquisition.sidecar_file is not None:
         add_bids_mri_sidecar_file_parameters(env, acquisition.sidecar_file, file_parameters)
         json_loris_path = get_loris_bids_file_path(
-            import_env,
+            importer,
             session,
             bids_info.data_type,
             acquisition.sidecar_file.path,
@@ -143,22 +144,26 @@ def import_bids_mri_acquisition(
 
     for aux_file_type, aux_file_path in aux_file_paths:
         aux_file_hash = compute_file_blake2b_hash(aux_file_path)
-        aux_file_loris_path = get_loris_bids_file_path(import_env, session, bids_info.data_type, aux_file_path)
+        aux_file_loris_path = get_loris_bids_file_path(importer, session, bids_info.data_type, aux_file_path)
+        get_or_create_loris_bids_file(env, importer, aux_file_path, aux_file_loris_path)
         files_to_copy.append((aux_file_path, aux_file_loris_path))
         file_parameters[f'bids_{aux_file_type}']              = str(aux_file_loris_path)
         file_parameters[f'bids_{aux_file_type}_blake2b_hash'] = aux_file_hash
 
     # Copy the files on the file system.
     for copied_file_path, loris_copied_file_path in files_to_copy:
-        copy_loris_bids_file(import_env, copied_file_path, loris_copied_file_path)
+        copy_loris_bids_file(importer, copied_file_path, loris_copied_file_path)
 
     # Register the file and its parameters in the database.
 
+    bids_file = get_or_create_loris_bids_file(env, importer, acquisition.nifti_path, loris_file_path)
+
     file = register_mri_file(
         env,
         loris_file_path,
         file_type,
         session,
+        bids_file,
         scan_type,
         None,
         None,
diff --git a/python/loris_bids_importer/src/loris_bids_importer/print.py b/python/loris_bids_importer/src/loris_bids_importer/print.py
index 8d82be18d..55e069d4f 100644
--- a/python/loris_bids_importer/src/loris_bids_importer/print.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/print.py
@@ -2,7 +2,7 @@
 from lib.logging import log
 from loris_bids_utils.reader import BidsDatasetReader
 
-from loris_bids_importer.env import BidsImportEnv
+from loris_bids_importer.importer import BidsImporter
 
 
 def print_bids_info(env: Env, bids: BidsDatasetReader):
@@ -23,7 +23,7 @@ def print_bids_info(env: Env, bids: BidsDatasetReader):
         log(env, f"- {data_type_name}")
 
 
-def print_bids_import_summary(env: Env, import_env: BidsImportEnv):
+def print_bids_import_summary(env: Env, importer: BidsImporter):
     """
     Print a summary of this BIDS import process.
     """
@@ -31,8 +31,8 @@ def print_bids_import_summary(env: Env, import_env: BidsImportEnv):
     log(
         env,
         (
-            f"Processed {import_env.processed_acquisitions_count} acquisitions, including"
-            f" {import_env.imported_acquisitions_count} imports, {import_env.ignored_acquisitions_count} ignores, and"
-            f" {import_env.failed_acquisitions_count} errors."
+            f"Processed {importer.processed_acquisitions_count} acquisitions, including"
+            f" {importer.imported_acquisitions_count} imports, {importer.ignored_acquisitions_count} ignores, and"
+            f" {importer.failed_acquisitions_count} errors."
         ),
     )
diff --git a/python/loris_bids_importer/src/loris_bids_importer/scripts/import_bids_dataset.py b/python/loris_bids_importer/src/loris_bids_importer/scripts/import_bids_dataset.py
index 4a3cccca8..fb7262a52 100755
--- a/python/loris_bids_importer/src/loris_bids_importer/scripts/import_bids_dataset.py
+++ b/python/loris_bids_importer/src/loris_bids_importer/scripts/import_bids_dataset.py
@@ -7,12 +7,12 @@
 from lib.logging import log_error_exit
 from lib.lorisgetopt import LorisGetOpt
 
-from loris_bids_importer.args import Args
+from loris_bids_importer.importer import BidsImporterArgs
 from loris_bids_importer.main import import_bids_dataset
 
 
-def pack_args(options_dict: dict[str, Any]) -> Args:
-    return Args(
+def pack_args(options_dict: dict[str, Any]) -> BidsImporterArgs:
+    return BidsImporterArgs(
         source_bids_path = Path(options_dict['directory']['value']),
         type             = options_dict['type']['value'],
         bids_validation  = not options_dict['no-bids-validation']['value'],
diff --git a/revert-bids-tables.sql b/revert-bids-tables.sql
new file mode 100644
index 000000000..c1897327c
--- /dev/null
+++ b/revert-bids-tables.sql
@@ -0,0 +1,29 @@
+ALTER TABLE `physiological_file`
+  DROP FOREIGN KEY `physiological_file_head_shape_file_id_fk`,
+  ADD CONSTRAINT `physiological_file_head_shape_file_id_fk`
+    FOREIGN KEY (`HeadShapeFileID`) REFERENCES `meg_ctf_head_shape_file` (`ID`);
+
+ALTER TABLE `meg_ctf_head_shape_file`
+  DROP FOREIGN KEY `meg_ctf_head_shape_file_bids_info_id_fk`,
+  DROP KEY `meg_ctf_head_shape_file_bids_info_id_fk_idx`,
+  DROP COLUMN `InsertTime`,
+  DROP COLUMN `BidsInfoID`;
+
+ALTER TABLE `physiological_event_file`
+  DROP FOREIGN KEY `physiological_event_file_bids_info_id_fk`,
+  DROP KEY `physiological_event_file_bids_info_id_fk_idx`,
+  DROP COLUMN `BidsInfoID`;
+
+ALTER TABLE `physiological_file`
+  DROP FOREIGN KEY `physiological_file_bids_info_id_fk`,
+  DROP KEY `physiological_file_bids_info_id_fk_idx`,
+  DROP COLUMN `BidsInfoID`;
+
+ALTER TABLE `files`
+  DROP FOREIGN KEY `files_bids_info_id_fk`,
+  DROP KEY `files_bids_info_id_fk_idx`,
+  DROP COLUMN `BidsInfoID`;
+
+DROP TABLE `bids_file`;
+
+DROP TABLE `bids_dataset`;