diff --git a/AFQ/afq_bids_entities.json b/AFQ/afq_bids_entities.json
new file mode 100644
index 000000000..32fbf771b
--- /dev/null
+++ b/AFQ/afq_bids_entities.json
@@ -0,0 +1,22 @@
+{
+    "name": "bidsafq",
+    "entities": [
+      {
+        "name": "odfmodel",
+        "pattern": "[_/\\\\]+odfmodel-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "coordsys",
+        "pattern": "[_/\\\\]+coordsys-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "trkmethod",
+        "pattern": "[_/\\\\]+trkmethod-([a-zA-Z0-9]+)"
+      },
+      {
+        "name": "recogmethod",
+        "pattern": "[_/\\\\]+recogmethod-([a-zA-Z0-9]+)"
+      }
+    ]
+  }
+  
\ No newline at end of file
diff --git a/AFQ/api/group.py b/AFQ/api/group.py
index 7cdd2f1fb..0de25fab5 100644
--- a/AFQ/api/group.py
+++ b/AFQ/api/group.py
@@ -41,7 +41,7 @@
     using_afqb = False
 
 
-__all__ = ["GroupAFQ"]
+__all__ = ["GroupAFQ", "get_afq_bids_entities_fname"]
 
 
 logger = logging.getLogger('AFQ')
@@ -55,6 +55,11 @@ def clean_pandas_df(df):
     return df
 
 
+def get_afq_bids_entities_fname():
+    return op.dirname(op.dirname(op.abspath(
+        aus.__file__))) + "/afq_bids_entities.json"
+
+
 class GroupAFQ(object):
     f"""{AFQclass_doc}"""
 
diff --git a/AFQ/api/participant.py b/AFQ/api/participant.py
index d557ce3b6..11b95c483 100644
--- a/AFQ/api/participant.py
+++ b/AFQ/api/participant.py
@@ -1,6 +1,5 @@
 import nibabel as nib
 import os.path as op
-import os
 from time import time
 import logging
 from tqdm import tqdm
@@ -20,7 +19,8 @@
 from AFQ.tasks.tractography import get_tractography_plan
 from AFQ.tasks.segmentation import get_segmentation_plan
 from AFQ.tasks.viz import get_viz_plan
-from AFQ.utils.path import drop_extension, apply_cmd_to_afq_derivs
+from AFQ.tasks.utils import get_base_fname
+from AFQ.utils.path import apply_cmd_to_afq_derivs
 from AFQ.viz.utils import BEST_BUNDLE_ORIENTATIONS, trim, get_eye
 
 
@@ -104,9 +104,7 @@ def __init__(self,
             results_dir=output_dir,
             dwi_affine=nib.load(dwi_data_file).affine,
             bids_info=bids_info,
-            base_fname=op.join(
-                output_dir,
-                drop_extension(op.basename(dwi_data_file))),
+            base_fname=get_base_fname(output_dir, dwi_data_file),
             **kwargs)
         self.make_workflow()
 
diff --git a/AFQ/data/fetch.py b/AFQ/data/fetch.py
index ac1b965c7..c8040da5e 100644
--- a/AFQ/data/fetch.py
+++ b/AFQ/data/fetch.py
@@ -822,7 +822,8 @@ def read_cp_templates(as_img=True, resample_to=False):
         resample_to=resample_to)
 
     toc = time.perf_counter()
-    logger.debug(f'Cerebellar peduncles templates loaded in {toc - tic:0.4f} seconds')
+    logger.debug(
+        f'Cerebellar peduncles templates loaded in {toc - tic:0.4f} seconds')
 
     return template_dict
 
@@ -1084,7 +1085,7 @@ def organize_stanford_data(path=None, clear_previous_afq=None):
         else:
             apply_cmd_to_afq_derivs(
                 op.join(afq_folder, "sub-01/ses-01"),
-                op.join(afq_folder, "sub-01/ses-01/sub-01_ses-01_dwi"),
+                op.join(afq_folder, "sub-01/ses-01/sub-01_ses-01"),
                 dependent_on=clear_previous_afq)
 
     if not op.exists(derivatives_path):
diff --git a/AFQ/tasks/data.py b/AFQ/tasks/data.py
index 488aabbfa..318233665 100644
--- a/AFQ/tasks/data.py
+++ b/AFQ/tasks/data.py
@@ -124,7 +124,7 @@ def dti_fit(dti_params, gtab):
 
 
 @pimms.calc("dti_params")
-@as_file(suffix='_model-DTI_desc-diffmodel_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-diffmodel_dwi.nii.gz')
 @as_img
 def dti_params(brain_mask, data, gtab,
                bval, bvec, b0_threshold=50, robust_tensor_fitting=False):
@@ -172,7 +172,7 @@ def fwdti_fit(fwdti_params, gtab):
 
 
 @pimms.calc("fwdti_params")
-@as_file(suffix='_model-FWDTI_desc-diffmodel_dwi.nii.gz')
+@as_file(suffix='_odfmodel-FWDTI_desc-diffmodel_dwi.nii.gz')
 @as_img
 def fwdti_params(brain_mask, data, gtab):
     """
@@ -200,7 +200,7 @@ def dki_fit(dki_params, gtab):
 
 
 @pimms.calc("dki_params")
-@as_file(suffix='_model-DKI_desc-diffmodel_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-diffmodel_dwi.nii.gz')
 @as_img
 def dki_params(brain_mask, gtab, data):
     """
@@ -221,7 +221,7 @@ def dki_params(brain_mask, gtab, data):
 
 
 @pimms.calc("csd_params")
-@as_file(suffix='_model-CSD_desc-diffmodel_dwi.nii.gz')
+@as_file(suffix='_odfmodel-CSD_desc-diffmodel_dwi.nii.gz')
 @as_img
 def csd_params(dwi, brain_mask, gtab, data,
                csd_response=None, csd_sh_order=None,
@@ -285,7 +285,7 @@ def csd_params(dwi, brain_mask, gtab, data,
 
 
 @pimms.calc("csd_pmap")
-@as_file(suffix='_model-CSD_desc-APM_dwi.nii.gz')
+@as_file(suffix='_odfmodel-CSD_desc-APM_dwi.nii.gz')
 @as_img
 def anisotropic_power_map(csd_params):
     """
@@ -298,7 +298,7 @@ def anisotropic_power_map(csd_params):
 
 
 @pimms.calc("csd_ai")
-@as_file(suffix='_model-CSD_desc-AI_dwi.nii.gz')
+@as_file(suffix='_odfmodel-CSD_desc-AI_dwi.nii.gz')
 @as_img
 def csd_anisotropic_index(csd_params):
     """
@@ -334,7 +334,7 @@ def gq(base_fname, gtab, dwi_affine, data,
 
     GQ_shm, ASO, ISO = extract_odf(odf)
 
-    params_suffix = "_model-GQ_desc-diffmodel_dwi.nii.gz"
+    params_suffix = "_odfmodel-GQ_desc-diffmodel_dwi.nii.gz"
     params_fname = get_fname(base_fname, params_suffix)
     nib.save(nib.Nifti1Image(GQ_shm, dwi_affine), params_fname)
     write_json(
@@ -342,7 +342,7 @@ def gq(base_fname, gtab, dwi_affine, data,
         dict(GQSamplingLength=gq_sampling_length)
     )
 
-    ASO_suffix = "_model-GQ_desc-ASO_dwi.nii.gz"
+    ASO_suffix = "_odfmodel-GQ_desc-ASO_dwi.nii.gz"
     ASO_fname = get_fname(base_fname, ASO_suffix)
     nib.save(nib.Nifti1Image(ASO, dwi_affine), ASO_fname)
     write_json(
@@ -350,7 +350,7 @@ def gq(base_fname, gtab, dwi_affine, data,
         dict(GQSamplingLength=gq_sampling_length)
     )
 
-    ISO_suffix = "_model-GQ_desc-ISO_dwi.nii.gz"
+    ISO_suffix = "_odfmodel-GQ_desc-ISO_dwi.nii.gz"
     ISO_fname = get_fname(base_fname, ISO_suffix)
     nib.save(nib.Nifti1Image(ISO, dwi_affine), ISO_fname)
     write_json(
@@ -362,7 +362,7 @@ def gq(base_fname, gtab, dwi_affine, data,
 
 
 @pimms.calc("gq_pmap")
-@as_file(suffix='_model-GQ_desc-APM_dwi.nii.gz')
+@as_file(suffix='_odfmodel-GQ_desc-APM_dwi.nii.gz')
 @as_img
 def gq_pmap(gq_params):
     """
@@ -375,7 +375,7 @@ def gq_pmap(gq_params):
 
 
 @pimms.calc("gq_ai")
-@as_file(suffix='_model-GQ_desc-AI_dwi.nii.gz')
+@as_file(suffix='_odfmodel-GQ_desc-AI_dwi.nii.gz')
 @as_img
 def gq_ai(gq_params):
     """
@@ -406,7 +406,7 @@ def opdt_params(base_fname, data, gtab,
     opdt_model = shm.OpdtModel(gtab, opdt_sh_order)
     opdt_fit = opdt_model.fit(data, mask=brain_mask)
 
-    params_suffix = "_model-OPDT_desc-diffmodel_dwi.nii.gz"
+    params_suffix = "_odfmodel-OPDT_desc-diffmodel_dwi.nii.gz"
     params_fname = get_fname(base_fname, params_suffix)
     nib.save(nib.Nifti1Image(opdt_fit._shm_coef, dwi_affine), params_fname)
     write_json(
@@ -414,7 +414,7 @@ def opdt_params(base_fname, data, gtab,
         dict(sh_order=opdt_sh_order)
     )
 
-    GFA_suffix = "_model-OPDT_desc-GFA_dwi.nii.gz"
+    GFA_suffix = "_odfmodel-OPDT_desc-GFA_dwi.nii.gz"
     GFA_fname = get_fname(base_fname, GFA_suffix)
     nib.save(nib.Nifti1Image(opdt_fit.gfa, dwi_affine), GFA_fname)
     write_json(
@@ -426,7 +426,7 @@ def opdt_params(base_fname, data, gtab,
 
 
 @pimms.calc("opdt_pmap")
-@as_file(suffix='_model-OPDT_desc-APM_dwi.nii.gz')
+@as_file(suffix='_odfmodel-OPDT_desc-APM_dwi.nii.gz')
 @as_img
 def opdt_pmap(opdt_params):
     """
@@ -439,7 +439,7 @@ def opdt_pmap(opdt_params):
 
 
 @pimms.calc("opdt_ai")
-@as_file(suffix='_model-OPDT_desc-AI_dwi.nii.gz')
+@as_file(suffix='_odfmodel-OPDT_desc-AI_dwi.nii.gz')
 @as_img
 def opdt_ai(opdt_params):
     """
@@ -470,7 +470,7 @@ def csa_params(base_fname, data, gtab,
     csa_model = shm.CsaOdfModel(gtab, csa_sh_order)
     csa_fit = csa_model.fit(data, mask=brain_mask)
 
-    params_suffix = "_model-CSA_desc-diffmodel_dwi.nii.gz"
+    params_suffix = "_odfmodel-CSA_desc-diffmodel_dwi.nii.gz"
     params_fname = get_fname(base_fname, params_suffix)
     nib.save(nib.Nifti1Image(csa_fit._shm_coef, dwi_affine), params_fname)
     write_json(
@@ -478,7 +478,7 @@ def csa_params(base_fname, data, gtab,
         dict(sh_order=csa_sh_order)
     )
 
-    GFA_suffix = "_model-CSA_desc-GFA_dwi.nii.gz"
+    GFA_suffix = "_odfmodel-CSA_desc-GFA_dwi.nii.gz"
     GFA_fname = get_fname(base_fname, GFA_suffix)
     nib.save(nib.Nifti1Image(csa_fit.gfa, dwi_affine), GFA_fname)
     write_json(
@@ -490,7 +490,7 @@ def csa_params(base_fname, data, gtab,
 
 
 @pimms.calc("csa_pmap")
-@as_file(suffix='_model-CSA_desc-APM_dwi.nii.gz')
+@as_file(suffix='_odfmodel-CSA_desc-APM_dwi.nii.gz')
 @as_img
 def csa_pmap(csa_params):
     """
@@ -503,7 +503,7 @@ def csa_pmap(csa_params):
 
 
 @pimms.calc("csa_ai")
-@as_file(suffix='_model-CSA_desc-AI_dwi.nii.gz')
+@as_file(suffix='_odfmodel-CSA_desc-AI_dwi.nii.gz')
 @as_img
 def csa_ai(csa_params):
     """
@@ -516,7 +516,7 @@ def csa_ai(csa_params):
 
 
 @pimms.calc("fwdti_fa")
-@as_file(suffix='_model-FWDTI_desc-FA_dwi.nii.gz')
+@as_file(suffix='_odfmodel-FWDTI_desc-FA_dwi.nii.gz')
 @as_fit_deriv('FWDTI')
 def fwdti_fa(fwdti_tf):
     """
@@ -527,7 +527,7 @@ def fwdti_fa(fwdti_tf):
 
 
 @pimms.calc("fwdti_md")
-@as_file(suffix='_model-FWDTI_desc-MD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-FWDTI_desc-MD_dwi.nii.gz')
 @as_fit_deriv('FWDTI')
 def fwdti_md(fwdti_tf):
     """
@@ -537,7 +537,7 @@ def fwdti_md(fwdti_tf):
 
 
 @pimms.calc("fwdti_fwf")
-@as_file(suffix='_model-FWDTI_desc-FWF_dwi.nii.gz')
+@as_file(suffix='_odfmodel-FWDTI_desc-FWF_dwi.nii.gz')
 @as_fit_deriv('FWDTI')
 def fwdti_fwf(fwdti_tf):
     """
@@ -547,7 +547,7 @@ def fwdti_fwf(fwdti_tf):
 
 
 @pimms.calc("dti_fa")
-@as_file(suffix='_model-DTI_desc-FA_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-FA_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_fa(dti_tf):
     """
@@ -587,7 +587,7 @@ def dti_lt(dti_tf, dwi_affine):
 
 
 @pimms.calc("dti_cfa")
-@as_file(suffix='_model-DTI_desc-CFA_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-CFA_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_cfa(dti_tf):
     """
@@ -598,7 +598,7 @@ def dti_cfa(dti_tf):
 
 
 @pimms.calc("dti_pdd")
-@as_file(suffix='_model-DTI_desc-PDD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-PDD_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_pdd(dti_tf):
     """
@@ -612,7 +612,7 @@ def dti_pdd(dti_tf):
 
 
 @pimms.calc("dti_md")
-@as_file('_model-DTI_desc-MD_dwi.nii.gz')
+@as_file('_odfmodel-DTI_desc-MD_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_md(dti_tf):
     """
@@ -623,7 +623,7 @@ def dti_md(dti_tf):
 
 
 @pimms.calc("dti_ga")
-@as_file(suffix='_model-DTI_desc-GA_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-GA_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_ga(dti_tf):
     """
@@ -634,7 +634,7 @@ def dti_ga(dti_tf):
 
 
 @pimms.calc("dti_rd")
-@as_file(suffix='_model-DTI_desc-RD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-RD_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_rd(dti_tf):
     """
@@ -645,7 +645,7 @@ def dti_rd(dti_tf):
 
 
 @pimms.calc("dti_ad")
-@as_file(suffix='_model-DTI_desc-AD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DTI_desc-AD_dwi.nii.gz')
 @as_fit_deriv('DTI')
 def dti_ad(dti_tf):
     """
@@ -704,7 +704,7 @@ def dki_lt(dki_tf, dwi_affine):
 
 
 @pimms.calc("dki_fa")
-@as_file('_model-DKI_desc-FA_dwi.nii.gz')
+@as_file('_odfmodel-DKI_desc-FA_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_fa(dki_tf):
     """
@@ -715,7 +715,7 @@ def dki_fa(dki_tf):
 
 
 @pimms.calc("dki_md")
-@as_file('_model-DKI_desc-MD_dwi.nii.gz')
+@as_file('_odfmodel-DKI_desc-MD_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_md(dki_tf):
     """
@@ -726,7 +726,7 @@ def dki_md(dki_tf):
 
 
 @pimms.calc("dki_awf")
-@as_file('_model-DKI_desc-AWF_dwi.nii.gz')
+@as_file('_odfmodel-DKI_desc-AWF_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_awf(dki_params,
             sphere='repulsion100', gtol=1e-2):
@@ -754,7 +754,7 @@ def dki_awf(dki_params,
 
 
 @pimms.calc("dki_mk")
-@as_file('_model-DKI_desc-MK_dwi.nii.gz')
+@as_file('_odfmodel-DKI_desc-MK_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_mk(dki_tf):
     """
@@ -765,7 +765,7 @@ def dki_mk(dki_tf):
 
 
 @pimms.calc("dki_ga")
-@as_file(suffix='_model-DKI_desc-GA_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-GA_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_ga(dki_tf):
     """
@@ -776,7 +776,7 @@ def dki_ga(dki_tf):
 
 
 @pimms.calc("dki_rd")
-@as_file(suffix='_model-DKI_desc-RD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-RD_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_rd(dki_tf):
     """
@@ -787,7 +787,7 @@ def dki_rd(dki_tf):
 
 
 @pimms.calc("dki_ad")
-@as_file(suffix='_model-DKI_desc-AD_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-AD_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_ad(dki_tf):
     """
@@ -798,7 +798,7 @@ def dki_ad(dki_tf):
 
 
 @pimms.calc("dki_rk")
-@as_file(suffix='_model-DKI_desc-RK_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-RK_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_rk(dki_tf):
     """
@@ -809,7 +809,7 @@ def dki_rk(dki_tf):
 
 
 @pimms.calc("dki_ak")
-@as_file(suffix='_model-DKI_desc-AK_dwi.nii.gz')
+@as_file(suffix='_odfmodel-DKI_desc-AK_dwi.nii.gz')
 @as_fit_deriv('DKI')
 def dki_ak(dki_tf):
     """
diff --git a/AFQ/tasks/utils.py b/AFQ/tasks/utils.py
index 1df2b3b39..d764f7dde 100644
--- a/AFQ/tasks/utils.py
+++ b/AFQ/tasks/utils.py
@@ -1,7 +1,25 @@
+from AFQ.utils.path import drop_extension
 import os.path as op
 import inspect
 
-__all__ = ["get_fname", "with_name"]
+__all__ = ["get_fname", "with_name", "get_base_fname"]
+
+
+def get_base_fname(output_dir, dwi_data_file):
+    # setup up path and base file name for outputs
+    # remove suffix and desc from dwi data file name
+    used_key_list = ["desc", "space", "to", "from"]
+    dwi_dfile_no_ext = op.join(
+        output_dir,
+        drop_extension(op.basename(dwi_data_file)))
+    fname = op.dirname(dwi_dfile_no_ext) + "/"
+    for key_val_pair in op.basename(dwi_dfile_no_ext).split("_"):
+        if "-" in key_val_pair:
+            key = key_val_pair.split("-")[0]
+            if key not in used_key_list:
+                fname = fname + key_val_pair + "_"
+    fname = fname[:-1]
+    return fname
 
 
 def get_fname(base_fname, suffix,
@@ -11,11 +29,11 @@ def get_fname(base_fname, suffix,
         odf_model = tracking_params['odf_model']
         directions = tracking_params['directions']
         fname = fname + (
-            f'_space-RASMM_model-{directions+odf_model}'
+            f'_coordsys-RASMM_trkmethod-{directions+odf_model}'
         )
     if segmentation_params is not None and 'seg_algo' in segmentation_params:
         seg_algo = segmentation_params['seg_algo']
-        fname = fname + f"_algo-{seg_algo}"
+        fname = fname + f"_recogmethod-{seg_algo}"
 
     return fname + suffix
 
diff --git a/AFQ/tests/test_api.py b/AFQ/tests/test_api.py
index 788005895..c431888c8 100644
--- a/AFQ/tests/test_api.py
+++ b/AFQ/tests/test_api.py
@@ -427,7 +427,7 @@ def test_AFQ_anisotropic():
     myafq.export("mapping")
     assert op.exists(op.join(
         myafq.export("results_dir")["01"],
-        'sub-01_ses-01_dwi_model-CSD_desc-APM_dwi.nii.gz'))
+        'sub-01_ses-01_odfmodel-CSD_desc-APM_dwi.nii.gz'))
 
 
 def test_API_type_checking():
@@ -822,11 +822,11 @@ def test_AFQ_data_waypoint():
 
     mapping_file = op.join(
         myafq.export("results_dir"),
-        'sub-01_ses-01_dwi_desc-mapping_from-DWI_to-MNI_xform.nii.gz')
+        'sub-01_ses-01_desc-mapping_from-DWI_to-MNI_xform.nii.gz')
     nib.save(mapping, mapping_file)
     reg_prealign_file = op.join(
         myafq.export("results_dir"),
-        'sub-01_ses-01_dwi_desc-prealign_from-DWI_to-MNI_xform.npy')
+        'sub-01_ses-01_desc-prealign_from-DWI_to-MNI_xform.npy')
     np.save(reg_prealign_file, np.eye(4))
 
     # Test ROI exporting:
@@ -834,7 +834,7 @@ def test_AFQ_data_waypoint():
     assert op.exists(op.join(
         myafq.export("results_dir"),
         'ROIs',
-        'sub-01_ses-01_dwi_space-subject_desc-CSTRinclude1_mask.json'))
+        'sub-01_ses-01_space-subject_desc-CSTRinclude1_mask.json'))
 
     seg_sft = aus.SegmentedSFT.fromfile(
         myafq.export("bundles"))
@@ -845,7 +845,7 @@ def test_AFQ_data_waypoint():
     assert op.exists(op.join(
         myafq.export("results_dir"),
         'bundles',
-        'sub-01_ses-01_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-SLFL_tractography.trk'))  # noqa
+        'sub-01_ses-01_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-SLFL_tractography.trk'))  # noqa
 
     tract_profile_fname = myafq.export("profiles")
     tract_profiles = pd.read_csv(tract_profile_fname)
@@ -858,12 +858,12 @@ def test_AFQ_data_waypoint():
     assert op.exists(op.join(
         myafq.export("results_dir"),
         "viz_bundles",
-        'sub-01_ses-01_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-SLFLviz_dwi.html'))  # noqa
+        'sub-01_ses-01_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-SLFLviz_dwi.html'))  # noqa
 
     assert op.exists(op.join(
         myafq.export("results_dir"),
         "viz_bundles",
-        'sub-01_ses-01_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-SLFLviz_dwi.html'))  # noqa
+        'sub-01_ses-01_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-SLFLviz_dwi.html'))  # noqa
 
     # Before we run the CLI, we'll remove the bundles and ROI folders, to see
     # that the CLI generates them
@@ -936,9 +936,9 @@ def test_AFQ_data_waypoint():
     assert op.exists(op.join(
         results_dir,
         'ROIs',
-        'sub-01_ses-01_dwi_space-subject_desc-SLFLinclude1_mask.json'))
+        'sub-01_ses-01_space-subject_desc-SLFLinclude1_mask.json'))
 
     assert op.exists(op.join(
         results_dir,
         'bundles',
-        'sub-01_ses-01_dwi_space-RASMM_model-probCSD_algo-AFQ_desc-SLFL_tractography.trk'))  # noqa
+        'sub-01_ses-01_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-SLFL_tractography.trk'))  # noqa
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 4692697be..bc3915cbb 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -235,5 +235,7 @@
 # Auto API
 autoapi_type = 'python'
 autoapi_dirs = ['../../AFQ']
-autoapi_ignore = ['*test*', '*_fixes*', '*version*', 'pyAFQ', 'License']
+autoapi_ignore = [
+    '*test*', '*_fixes*', '*version*',
+    'pyAFQ', 'License', 'afq_bids_entities.json']
 autoapi_root = 'reference/api'
diff --git a/examples/tutorial_examples/plot_bids_layout.py b/examples/tutorial_examples/plot_bids_layout.py
index d0c6e8ac1..4b9eb698b 100644
--- a/examples/tutorial_examples/plot_bids_layout.py
+++ b/examples/tutorial_examples/plot_bids_layout.py
@@ -25,8 +25,8 @@
 import os
 import os.path as op
 
-from AFQ.api.group import GroupAFQ
 import AFQ.api.bundle_dict as abd
+from AFQ.api.group import GroupAFQ, get_afq_bids_entities_fname
 import AFQ.data.fetch as afd
 
 
@@ -35,7 +35,7 @@
 #  `pyBIDS <https://bids-standard.github.io/pybids/>`_.
 
 import bids
-
+from bids.layout import BIDSLayout
 
 ##########################################################################
 # We start with some example data. The data we will use here is
@@ -256,3 +256,16 @@
 #    file contains the right names for the pipeline. See above for an example
 #    of that.
 # 2. File naming convention doesn't uniquely identify file with bids filters.
+
+
+##########################################################################
+# The outputs of AFQ are also BIDS compatible. However, we use some
+# custom entities, which need to be loaded. Here we demonstrate how
+# to load the afq entities with get_afq_bids_entities_fname()
+# and then show all files with the key-value pair recogmethod-AFQ
+
+layout = BIDSLayout(bids_path)
+layout.add_derivatives(
+    f'{bids_path}/derivatives/afq',
+    config=['bids', 'derivatives', get_afq_bids_entities_fname()])
+print(layout.get(recogmethod="AFQ", return_type="filename"))