diff --git a/mriqc/cli/parser.py b/mriqc/cli/parser.py
index de711c9d..bad91cdc 100644
--- a/mriqc/cli/parser.py
+++ b/mriqc/cli/parser.py
@@ -448,7 +448,7 @@ def parse_args(args=None, namespace=None):
     from logging import DEBUG
     from contextlib import suppress
 
-    from mriqc.utils.bids import collect_bids_data
+    from niworkflows.utils.bids import collect_data, DEFAULT_BIDS_QUERIES
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
@@ -520,20 +520,29 @@ def parse_args(args=None, namespace=None):
     config.workflow.analysis_level = list(analysis_level)
 
     # List of files to be run
-    bids_filters = {
-        "participant_label": config.execution.participant_label,
-        "session": config.execution.session_id,
-        "run": config.execution.run_id,
-        "task": config.execution.task_id,
-        "bids_type": config.execution.modalities,
-    }
-    config.workflow.inputs = {
-        mod: files
-        for mod, files in collect_bids_data(
-            config.execution.layout, **bids_filters
-        ).items()
-        if files
+    lc_modalities = [mod.lower() for mod in config.execution.modalities]
+
+    bids_filters = (
+        {mod: {"run": config.execution.run_id} for mod in lc_modalities}
+        if config.execution.run_id
+        else {}
+    )
+
+    bids_dataset, _ = collect_data(
+        config.execution.layout,
+        config.execution.participant_label,
+        session_id=config.execution.session_id,
+        task=config.execution.task_id,
+        group_me=False,  # for backward compatibility
+        bids_filters=bids_filters,
+        queries={mod: DEFAULT_BIDS_QUERIES[mod] for mod in lc_modalities}
+    )
+
+    # Drop empty queries
+    bids_dataset = {
+        mod: files for mod, files in bids_dataset.items() if files
     }
+    config.workflow.inputs = bids_dataset
 
     # Check the query is not empty
     if not list(config.workflow.inputs.values()):
@@ -546,7 +555,9 @@ def parse_args(args=None, namespace=None):
         )
 
     # Check no DWI or others are sneaked into MRIQC
-    unknown_mods = set(config.workflow.inputs.keys()) - set(config.SUPPORTED_SUFFIXES)
+    unknown_mods = set(config.workflow.inputs.keys()) - set(
+        suffix.lower() for suffix in config.SUPPORTED_SUFFIXES
+    )
     if unknown_mods:
         parser.error(
             "MRIQC is unable to process the following modalities: "
diff --git a/mriqc/utils/__init__.py b/mriqc/utils/__init__.py
index ce449276..e69de29b 100644
--- a/mriqc/utils/__init__.py
+++ b/mriqc/utils/__init__.py
@@ -1,28 +0,0 @@
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-#
-# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# We support and encourage derived works from this project, please read
-# about our expectations at
-#
-#     https://www.nipreps.org/community/licensing/
-#
-"""Module utils.misc contains utilities."""
-from mriqc.utils.bids import collect_bids_data
-
-__all__ = [
-    "collect_bids_data",
-]
diff --git a/mriqc/utils/bids.py b/mriqc/utils/bids.py
index 5ddc40b4..4ab14265 100644
--- a/mriqc/utils/bids.py
+++ b/mriqc/utils/bids.py
@@ -23,49 +23,11 @@
 """PyBIDS tooling."""
 import json
 import os
-from collections import defaultdict
 from pathlib import Path
 
-from bids.utils import listify
-
 DOI = "https://doi.org/10.1371/journal.pone.0184661"
 
 
-def collect_bids_data(
-    layout,
-    bids_type,
-    participant_label=None,
-    session=None,
-    run=None,
-    task=None,
-):
-    """Get files in dataset"""
-
-    basequery = {
-        "subject": participant_label,
-        "session": session,
-        "task": task,
-        "run": run,
-        "datatype": "func",
-        "return_type": "file",
-        "extension": ["nii", "nii.gz"],
-    }
-    # Filter empty lists, strings, zero runs, and Nones
-    basequery = {k: v for k, v in basequery.items() if v}
-
-    # Start querying
-    imaging_data = defaultdict(list, {})
-    for btype in listify(bids_type):
-        _entities = basequery.copy()
-        _entities["suffix"] = btype
-        if btype in ("T1w", "T2w", "dwi"):
-            _entities["datatype"] = "dwi" if btype == "dwi" else "anat"
-            _entities.pop("task", None)
-        imaging_data[btype] = layout.get(**_entities)
-
-    return imaging_data
-
-
 def write_bidsignore(deriv_dir):
     from mriqc.config import SUPPORTED_SUFFIXES
     bids_ignore = [
diff --git a/mriqc/workflows/anatomical/base.py b/mriqc/workflows/anatomical/base.py
index 327ae79f..400dee06 100644
--- a/mriqc/workflows/anatomical/base.py
+++ b/mriqc/workflows/anatomical/base.py
@@ -87,7 +87,7 @@ def anat_qc_workflow(name="anatMRIQC"):
 
     """
 
-    dataset = config.workflow.inputs.get("T1w", []) + config.workflow.inputs.get("T2w", [])
+    dataset = config.workflow.inputs.get("t1w", []) + config.workflow.inputs.get("t2w", [])
 
     message = BUILDING_WORKFLOW.format(
         modality="anatomical",
diff --git a/mriqc/workflows/core.py b/mriqc/workflows/core.py
index 8f654d42..5aa53088 100644
--- a/mriqc/workflows/core.py
+++ b/mriqc/workflows/core.py
@@ -28,7 +28,7 @@
 from mriqc.workflows.functional.base import fmri_qc_workflow
 from mriqc.workflows.diffusion.base import dmri_qc_workflow
 
-ANATOMICAL_KEYS = "T1w", "T2w"
+ANATOMICAL_KEYS = "t1w", "t2w"
 FMRI_KEY = "bold"
 DMRI_KEY = "dwi"