diff --git a/docs/workflows.rst b/docs/workflows.rst
index 4a3246bef..60ea69569 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -62,6 +62,7 @@ is presented below:
         use_aroma=False,
         use_bbr=True,
         use_syn=True,
+        bids_filters=None,
     )
 
 T1w/T2w preprocessing
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 70bc1f5a3..224b5d9ed 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -10,6 +10,7 @@
 import gc
 import uuid
 import warnings
+import json
 from argparse import ArgumentParser
 from argparse import ArgumentDefaultsHelpFormatter
 from multiprocessing import cpu_count
@@ -76,6 +77,11 @@ def get_parser():
     # Re-enable when option is actually implemented
     # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
     #                     help='select a specific run to be processed')
+    g_bids.add_argument(
+        '--bids-filter-file', action='store', type=Path, metavar='PATH',
+        help='a JSON file describing custom BIDS input filter using pybids '
+             '{<suffix>:{<entity>:<filter>,...},...} '
+             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
     g_bids.add_argument('-t', '--task-id', action='store',
                         help='select a specific task to be processed')
     g_bids.add_argument('--echo-idx', action='store', type=int,
@@ -500,6 +506,7 @@ def build_workflow(opts, retval):
     bids_dir = opts.bids_dir.resolve()
     output_dir = opts.output_dir.resolve()
     work_dir = opts.work_dir.resolve()
+    bids_filters = json.loads(opts.bids_filter_file.read_text()) if opts.bids_filter_file else None
 
     if opts.clean_workdir:
         from niworkflows.utils.misc import clean_directory
@@ -675,6 +682,7 @@ def build_workflow(opts, retval):
         use_bbr=opts.use_bbr,
         use_syn=opts.use_syn_sdc,
         work_dir=str(work_dir),
+        bids_filters=bids_filters,
     )
     retval['return_code'] = 0
 
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 19d2bf628..c0ceb5ebf 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -67,12 +67,14 @@ def init_fmriprep_wf(
     use_bbr,
     use_syn,
     work_dir,
+    bids_filters,
 ):
     """
     Build *fMRIPrep*'s pipeline.
 
     This workflow organizes the execution of FMRIPREP, with a sub-workflow for
     each subject.
+
     If FreeSurfer's ``recon-all`` is to be run, a corresponding folder is created
     and populated with any needed template subjects under the derivatives folder.
 
@@ -129,6 +131,7 @@ def init_fmriprep_wf(
                 use_bbr=True,
                 use_syn=True,
                 work_dir='.',
+                bids_filters=None,
             )
 
 
@@ -213,6 +216,9 @@ def init_fmriprep_wf(
         If fieldmaps are present and enabled, this is not run, by default.
     work_dir : str
         Directory in which to store workflow execution state and temporary files
+    bids_filters : dict
+        Provides finer specification of the pipeline input files using pybids entities filters.
+        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     """
     fmriprep_wf = Workflow(name='fmriprep_wf')
@@ -265,6 +271,7 @@ def init_fmriprep_wf(
             use_aroma=use_aroma,
             use_bbr=use_bbr,
             use_syn=use_syn,
+            bids_filters=bids_filters,
         )
 
         single_subject_wf.config['execution']['crashdump_dir'] = (
@@ -316,6 +323,7 @@ def init_single_subject_wf(
     use_aroma,
     use_bbr,
     use_syn,
+    bids_filters,
 ):
     """
     This workflow organizes the preprocessing pipeline for a single subject.
@@ -377,6 +385,7 @@ def init_single_subject_wf(
                 use_aroma=False,
                 use_bbr=True,
                 use_syn=True,
+                bids_filters=None,
             )
 
     Parameters
@@ -463,6 +472,9 @@ def init_single_subject_wf(
     use_syn : bool
         **Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
         If fieldmaps are present and enabled, this is not run, by default.
+    bids_filters : dict
+        Provides finer specification of the pipeline input files using pybids entities filters.
+        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     Inputs
     ------
@@ -477,7 +489,8 @@ def init_single_subject_wf(
             'bold': ['/completely/made/up/path/sub-01_task-nback_bold.nii.gz']
         }
     else:
-        subject_data = collect_data(layout, subject_id, task_id, echo_idx)[0]
+        subject_data = collect_data(layout, subject_id, task_id, echo_idx,
+                                    bids_filters=bids_filters)[0]
 
     # Make sure we always go through these two checks
     if not anat_only and subject_data['bold'] == []:
diff --git a/setup.cfg b/setup.cfg
index bfbeecc42..e9dd0d5e5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -24,14 +24,14 @@ install_requires =
     nibabel >= 3.0.1
     nipype >=1.3.1
     nitime
-    niworkflows ~= 1.1.6
+    niworkflows @ git+https://github.com/poldracklab/niworkflows.git@edeea81352f3f2b276f11e42e7829e1c5a03770f
     numpy
     pandas
     psutil >=5.4
     pybids ~= 0.9.4
     pyyaml
     sdcflows ~=1.1.0
-    smriprep ~= 0.5.1
+    smriprep @ git+https://github.com/poldracklab/smriprep.git@07a7ba3fce8a9953923bcd0fa6ffbffac401208d
     tedana >=0.0.5
     templateflow ~= 0.4.2rc1
 test_requires =