From 94a92cce1504cf7509d7082f832bfe158bc913b4 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Mon, 23 Jan 2023 16:48:07 -0500
Subject: [PATCH 01/32] Add `cbma_workflow` function

---
 nimare/results.py              |  2 +-
 nimare/tests/test_workflows.py | 41 +++++++++++++++++
 nimare/workflows/__init__.py   |  3 +-
 nimare/workflows/cbma.py       | 84 ++++++++++++++++++++++++++++++++++
 4 files changed, 128 insertions(+), 2 deletions(-)
 create mode 100644 nimare/workflows/cbma.py

diff --git a/nimare/results.py b/nimare/results.py
index 25cb034ff..57514e780 100644
--- a/nimare/results.py
+++ b/nimare/results.py
@@ -148,7 +148,7 @@ def save_tables(self, output_dir=".", prefix="", prefix_sep="_", names=None):
         tables = {k: self.tables[k] for k in names}
 
         for tabletype, table in tables.items():
-            filename = prefix + tables + ".tsv"
+            filename = prefix + tabletype + ".tsv"
             outpath = os.path.join(output_dir, filename)
             table.to_csv(outpath, sep="\t", index=False)
 
diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 98de585a6..471567e6c 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -1,7 +1,11 @@
 """Test nimare.workflows."""
 import os.path as op
 
+import nimare
 from nimare import cli, workflows
+from nimare.correct import FWECorrector
+from nimare.diagnostics import FocusCounter
+from nimare.meta.cbma.ale import ALE
 from nimare.tests.utils import get_test_data_path
 
 
@@ -81,3 +85,40 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
         ]
     )
     assert op.isfile(op.join(tmpdir, f"{prefix}_group2_input_coordinates.txt"))
+
+
+def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
+    """Run smoke test for CBMA workflow."""
+    tmpdir = tmp_path_factory.mktemp("test_cbma_workflow_function_smoke")
+
+    # Initialize estimator, corrector and diagnostic classes
+    est = ALE(null_method="approximate")
+    corr = FWECorrector(method="montecarlo", n_iters=100)
+    diag = FocusCounter()
+
+    cres = workflows.cbma_workflow(
+        testdata_cbma_full,
+        meta_estimator=est,
+        corrector=corr,
+        diagnostics=(diag,),
+        output_dir=tmpdir,
+    )
+
+    assert isinstance(cres, nimare.results.MetaResult)
+
+    assert "cluster_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "cluster_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "cluster_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "FocusCounter_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "FocusCounter_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "FocusCounter_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
+
+    for imgtype in cres.maps.keys():
+        filename = imgtype + ".nii.gz"
+        outpath = op.join(tmpdir, filename)
+        assert op.isfile(outpath)
+
+    for tabletype in cres.tables.keys():
+        filename = tabletype + ".tsv"
+        outpath = op.join(tmpdir, filename)
+        assert op.isfile(outpath)
diff --git a/nimare/workflows/__init__.py b/nimare/workflows/__init__.py
index ecc0c2ab6..4c18a433c 100644
--- a/nimare/workflows/__init__.py
+++ b/nimare/workflows/__init__.py
@@ -1,6 +1,7 @@
 """Common meta-analytic workflows."""
 
 from .ale import ale_sleuth_workflow
+from .cbma import cbma_workflow
 from .macm import macm_workflow
 
-__all__ = ["ale_sleuth_workflow", "macm_workflow"]
+__all__ = ["ale_sleuth_workflow", "cbma_workflow", "macm_workflow"]
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
new file mode 100644
index 000000000..b5bef791f
--- /dev/null
+++ b/nimare/workflows/cbma.py
@@ -0,0 +1,84 @@
+"""Workflow for running an coordinates-based meta-analysis from a NiMARE database."""
+import logging
+
+from nilearn import reporting
+
+from nimare.correct import FWECorrector
+from nimare.diagnostics import FocusCounter
+from nimare.meta import ALE
+
+LGR = logging.getLogger(__name__)
+
+
+def cbma_workflow(
+    dataset,
+    meta_estimator=ALE(),
+    corrector=FWECorrector(),
+    diagnostics=(FocusCounter(),),
+    output_dir=None,
+):
+    """Compose a coordinate-based meta-analysis workflow.
+
+    .. versionadded:: 0.0.14
+
+    This workflow performs a coordinate-based meta-analysis, multiple comparison correction,
+    and diagnosis analysis on corrected meta-analytic images.
+
+    Parameters
+    ----------
+    dataset : :obj:`~nimare.dataset.Dataset`
+        Dataset for which to run meta-analyses to generate maps.
+    meta_estimator : :class:`~nimare.base.CBMAEstimator`, optional
+        Meta-analysis estimator. Default is :class:`~nimare.meta.cbma.ale.ALE`.
+    meta_corrector : :class:`~nimare.correct.Corrector`, optional
+        Meta-analysis corrector. Default is :class:`~nimare.correct.FWECorrector`.
+    diagnostics : :obj:`tuple`, optional
+        Tuple of meta-analysis diagnostic classes.
+        Default is :class:`~nimare.diagnostics.FocusCounter`.
+    output_dir : :obj:`str`, optional
+        Output directory in which to save results. If the directory doesn't
+        exist, it will be created. Default is None (the results are not saved).
+
+    Returns
+    -------
+    :obj:`~nimare.results.MetaResult`
+        Results of Estimator and Corrector fitting with cluster and diagnostic tables.
+    """
+    LGR.info("Performing meta-analysis...")
+    results = meta_estimator.fit(dataset)
+
+    LGR.info("Performing correction on meta-analysis...")
+    corr_results = corrector.transform(results)
+
+    for img_key in corr_results.maps.keys():
+        # Save cluster table only for z maps
+        if img_key.startswith("z_"):
+            cbma_img = corr_results.get_map(img_key)
+
+            LGR.info("Generating cluster tables...")
+            cluster_df = reporting.get_clusters_table(cbma_img, stat_threshold=0)
+            # Remove prefix from name
+            img_name = "_".join(img_key.split("_")[1:])
+
+            if not cluster_df.empty:
+                clust_tbl_name = f"cluster_{img_name}"
+                corr_results.tables[clust_tbl_name] = cluster_df
+
+            # Run diagnostic on corrected z maps
+            if "_corr-" in img_key:
+                for diagnostic in diagnostics:
+                    diagnostic.target_image = img_key
+
+                    LGR.info("Performing diagnostic on corrected meta-analysis...")
+                    count_df, _ = diagnostic.transform(corr_results)
+
+                    if not count_df.empty:
+                        diag_tbl_name = f"{diagnostic.__class__.__name__}_{img_name}"
+                        corr_results.tables[diag_tbl_name] = count_df
+
+    if output_dir is not None:
+        LGR.info(f"Saving meta-result object to {output_dir}...")
+        corr_results.save_maps(output_dir=output_dir)
+        corr_results.save_tables(output_dir=output_dir)
+
+    return corr_results

From f3411117cff28d70b67b865cc1bf81f1da62d7bf Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Mon, 23 Jan 2023 16:57:25 -0500
Subject: [PATCH 02/32] Fix typo

---
 nimare/workflows/cbma.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index b5bef791f..9d511f4df 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -22,7 +22,7 @@ def cbma_workflow(
     .. versionadded:: 0.0.14
 
     This workflow performs a coordinate-based meta-analysis, multiple comparison correction,
-    and diagnosis analysis on corrected meta-analytic images.
+    and diagnostics analyses on corrected meta-analytic images.
 
     Parameters
     ----------

From 24c8de1ec9891e871f1fe82d66487cbb0756b44c Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Wed, 25 Jan 2023 09:58:07 -0500
Subject: [PATCH 03/32] @jdkent Apply suggestions from code review

---
 nimare/workflows/cbma.py | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 9d511f4df..16aa49ba0 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -22,7 +22,7 @@ def cbma_workflow(
     .. versionadded:: 0.0.14
 
     This workflow performs a coordinate-based meta-analysis, multiple comparison correction,
-    and diagnostics analyses on corrected meta-analytic images.
+    and diagnostics analyses on corrected meta-analytic maps.
 
     Parameters
     ----------
@@ -50,34 +50,41 @@ def cbma_workflow(
     LGR.info("Performing correction on meta-analysis...")
     corr_results = corrector.transform(results)
 
+    LGR.info("Generating cluster tables and performing diagnostics on corrected meta-analyses...")
     for img_key in corr_results.maps.keys():
         # Save cluster table only for z maps
         if img_key.startswith("z_"):
             cbma_img = corr_results.get_map(img_key)
-
-            LGR.info("Generating cluster tables...")
             cluster_df = reporting.get_clusters_table(cbma_img, stat_threshold=0)
+
             # Remove prefix from name
             img_name = "_".join(img_key.split("_")[1:])
-
+            clust_tbl_name = f"cluster_{img_name}"
             if not cluster_df.empty:
-                clust_tbl_name = f"cluster_{img_name}"
                 corr_results.tables[clust_tbl_name] = cluster_df
+            else:
+                LGR.warn(
+                    f"Key {clust_tbl_name} will not be stored in MetaResult.tables dictionary."
+                )
 
             # Run diagnostic on corrected z maps
             if "_corr-" in img_key:
+                LGR.info("Performing diagnostic on corrected meta-analysis...")
                 for diagnostic in diagnostics:
                     diagnostic.target_image = img_key
-
-                    LGR.info("Performing diagnostic on corrected meta-analysis...")
                     count_df, _ = diagnostic.transform(corr_results)
 
+                    diag_tbl_name = f"{diagnostic.__class__.__name__}_{img_name}"
                     if not count_df.empty:
-                        diag_tbl_name = f"{diagnostic.__class__.__name__}_{img_name}"
                         corr_results.tables[diag_tbl_name] = count_df
+                    else:
+                        LGR.warn(
+                            f"Key {diag_tbl_name} will not be stored in "
+                            "MetaResult.tables dictionary."
+                        )
 
     if output_dir is not None:
-        LGR.info(f"Saving meta-result object to {output_dir}...")
+        LGR.info(f"Saving meta-analytic maps and tables result to {output_dir}...")
         corr_results.save_maps(output_dir=output_dir)
         corr_results.save_tables(output_dir=output_dir)
 

From 97779a5836297337bb5d57816d7d945de19ec3d4 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 14 Mar 2023 11:07:58 -0400
Subject: [PATCH 04/32] take clusters table from diagnostics

---
 nimare/tests/test_workflows.py | 10 +++----
 nimare/workflows/cbma.py       | 51 +++++++++++++---------------------
 2 files changed, 24 insertions(+), 37 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 471567e6c..65cb4d7fa 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -4,7 +4,7 @@
 import nimare
 from nimare import cli, workflows
 from nimare.correct import FWECorrector
-from nimare.diagnostics import FocusCounter
+from nimare.diagnostics import Jackknife
 from nimare.meta.cbma.ale import ALE
 from nimare.tests.utils import get_test_data_path
 
@@ -94,7 +94,7 @@ def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
     # Initialize estimator, corrector and diagnostic classes
     est = ALE(null_method="approximate")
     corr = FWECorrector(method="montecarlo", n_iters=100)
-    diag = FocusCounter()
+    diag = Jackknife()
 
     cres = workflows.cbma_workflow(
         testdata_cbma_full,
@@ -109,9 +109,9 @@ def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
     assert "cluster_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
     assert "cluster_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
     assert "cluster_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "FocusCounter_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "FocusCounter_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "FocusCounter_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "Jackknife_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "Jackknife_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "Jackknife_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
 
     for imgtype in cres.maps.keys():
         filename = imgtype + ".nii.gz"
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 16aa49ba0..adc0f368a 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -1,10 +1,8 @@
 """Workflow for running an coordinates-based meta-analysis from a NiMARE database."""
 import logging
 
-from nilearn import reporting
-
 from nimare.correct import FWECorrector
-from nimare.diagnostics import FocusCounter
+from nimare.diagnostics import Jackknife
 from nimare.meta import ALE
 
 LGR = logging.getLogger(__name__)
@@ -14,7 +12,7 @@ def cbma_workflow(
     dataset,
     meta_estimator=ALE(),
     corrector=FWECorrector(),
-    diagnostics=(FocusCounter(),),
+    diagnostics=(Jackknife(),),
     output_dir=None,
 ):
     """Compose a coordinate-based meta-analysis workflow.
@@ -50,38 +48,27 @@ def cbma_workflow(
     LGR.info("Performing correction on meta-analysis...")
     corr_results = corrector.transform(results)
 
-    LGR.info("Generating cluster tables and performing diagnostics on corrected meta-analyses...")
+    LGR.info("Generating clusters tables and performing diagnostics on corrected meta-analyses...")
     for img_key in corr_results.maps.keys():
         # Save cluster table only for z maps
-        if img_key.startswith("z_"):
-            cbma_img = corr_results.get_map(img_key)
-            cluster_df = reporting.get_clusters_table(cbma_img, stat_threshold=0)
-
-            # Remove prefix from name
+        if img_key.startswith("z_") and ("_corr-" in img_key):
             img_name = "_".join(img_key.split("_")[1:])
-            clust_tbl_name = f"cluster_{img_name}"
-            if not cluster_df.empty:
-                corr_results.tables[clust_tbl_name] = cluster_df
-            else:
-                LGR.warn(
-                    f"Key {clust_tbl_name} will not be stored in MetaResult.tables dictionary."
-                )
-
-            # Run diagnostic on corrected z maps
-            if "_corr-" in img_key:
-                LGR.info("Performing diagnostic on corrected meta-analysis...")
-                for diagnostic in diagnostics:
-                    diagnostic.target_image = img_key
-                    count_df, _ = diagnostic.transform(corr_results)
 
-                    diag_tbl_name = f"{diagnostic.__class__.__name__}_{img_name}"
-                    if not count_df.empty:
-                        corr_results.tables[diag_tbl_name] = count_df
-                    else:
-                        LGR.warn(
-                            f"Key {diag_tbl_name} will not be stored in "
-                            "MetaResult.tables dictionary."
-                        )
+            for diagnostic in diagnostics:
+                diagnostic.target_image = img_key
+                contribution_table, cluster_df, _ = diagnostic.transform(corr_results)
+
+                diag_name = diagnostic.__class__.__name__
+                clust_tbl_name = f"cluster_{img_name}"
+                diag_tbl_name = f"{diag_name}_{img_name}"
+                if not contribution_table.empty:
+                    corr_results.tables[clust_tbl_name] = cluster_df
+                    corr_results.tables[diag_tbl_name] = contribution_table
+                else:
+                    LGR.warn(
+                        f"Key {diag_tbl_name} and {clust_tbl_name} will not be stored in "
+                        "MetaResult.tables dictionary."
+                    )
 
     if output_dir is not None:
         LGR.info(f"Saving meta-analytic maps and tables result to {output_dir}...")

From 7af5adce2100b51e9af597982dca070db4caf86e Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 13:01:07 -0400
Subject: [PATCH 05/32] Add example to gallery

---
 docs/api.rst                                  |  1 +
 .../02_meta-analyses/10_plot_cbma_workflow.py | 84 +++++++++++++++++++
 nimare/workflows/cbma.py                      | 53 +++++++-----
 3 files changed, 117 insertions(+), 21 deletions(-)
 create mode 100644 examples/02_meta-analyses/10_plot_cbma_workflow.py

diff --git a/docs/api.rst b/docs/api.rst
index 39f4261b9..01e496322 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -310,6 +310,7 @@ For more information about fetching data from the internet, see :ref:`fetching t
 
    workflows.ale_sleuth_workflow
    workflows.macm_workflow
+   workflows.cbma_workflow
 
 
 .. _api_base_ref:
diff --git a/examples/02_meta-analyses/10_plot_cbma_workflow.py b/examples/02_meta-analyses/10_plot_cbma_workflow.py
new file mode 100644
index 000000000..b8626c375
--- /dev/null
+++ b/examples/02_meta-analyses/10_plot_cbma_workflow.py
@@ -0,0 +1,84 @@
+"""
+
+.. _cbma_workflow:
+
+====================================================
+Run a coordinate-based meta-analysis (CBMA) workflow
+====================================================
+
+NiMARE provides a plethora of tools for performing meta-analyses on neuroimaging data.
+Sometimes it's difficult to know where to start, especially if you're new to meta-analysis.
+This tutorial will walk you through using a CBMA workflow function which puts together
+the fundamental steps of a CBMA meta-analysis.
+"""
+import os
+from pprint import pprint
+
+import matplotlib.pyplot as plt
+from nilearn.plotting import plot_stat_map
+
+from nimare.dataset import Dataset
+from nimare.utils import get_resource_path
+from nimare.workflows import cbma_workflow
+
+###############################################################################
+# Load Dataset
+# -----------------------------------------------------------------------------
+
+dset_file = os.path.join(get_resource_path(), "nidm_pain_dset.json")
+dset = Dataset(dset_file)
+
+###############################################################################
+# Run CBMA Workflow
+# -----------------------------------------------------------------------------
+# The CBMA workflow function runs the following steps:
+#
+# 1. Runs a meta-analysis using the specified method (default: ALE)
+# 2. Applies a corrector to the meta-analysis results (default: FWECorrector)
+# 3. Generates cluster tables and runs diagnostics on the corrected results (default: Jackknife)
+#
+# All in one function call!
+
+result = cbma_workflow(dset)
+
+###############################################################################
+# Plot Results
+# -----------------------------------------------------------------------------
+# The CBMA workflow function returns a :class:`~nimare.results.MetaResult` object,
+# where you can access the corrected results of the meta-analysis and diagnostics tables.
+#
+# Corrected map:
+img = result.get_map("z_corr-FWE_method-bonferroni")
+plot_stat_map(
+    img,
+    cut_coords=4,
+    display_mode="z",
+    threshold=2.326,  # cluster-level p < .01, one-tailed
+    cmap="RdBu_r",
+    vmax=4,
+)
+plt.show()
+
+###############################################################################
+# Clusters table
+# ``````````````````````````````````````````````````````````````````````````````
+result.tables["z_corr-FWE_method-bonferroni_clust"]
+
+###############################################################################
+# Contribution table
+# ``````````````````````````````````````````````````````````````````````````````
+result.tables["z_corr-FWE_method-bonferroni_Jackknife"]
+
+###############################################################################
+# Methods
+# -----------------------------------------------------------------------------
+# The MetaResult object also provides boilerplate text automatically generated by NiMARE,
+# which is released under the `CC0 <https://creativecommons.org/publicdomain/zero/1.0/>`_ license.
+print("Description:")
+pprint(result.description_)
+
+###############################################################################
+# References
+# ``````````````````````````````````````````````````````````````````````````````
+print("References:")
+pprint(result.bibtex_)
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index adc0f368a..5acfbdaf3 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -1,5 +1,7 @@
 """Workflow for running an coordinates-based meta-analysis from a NiMARE database."""
+import itertools
 import logging
+import os.path as op
 
 from nimare.correct import FWECorrector
 from nimare.diagnostics import Jackknife
@@ -10,7 +12,7 @@
 
 def cbma_workflow(
     dataset,
-    meta_estimator=ALE(),
+    meta_estimator=ALE(null_method="approximate"),
     corrector=FWECorrector(),
     diagnostics=(Jackknife(),),
     output_dir=None,
@@ -49,30 +51,39 @@ def cbma_workflow(
     corr_results = corrector.transform(results)
 
     LGR.info("Generating clusters tables and performing diagnostics on corrected meta-analyses...")
-    for img_key in corr_results.maps.keys():
-        # Save cluster table only for z maps
-        if img_key.startswith("z_") and ("_corr-" in img_key):
-            img_name = "_".join(img_key.split("_")[1:])
+    img_keys = [
+        img_key
+        for img_key in corr_results.maps.keys()
+        if img_key.startswith("z_") and ("_corr-" in img_key)
+    ]
+    for img_key, diagnostic in itertools.product(img_keys, diagnostics):
+        diagnostic.target_image = img_key
+        contribution_table, clusters_table, _ = diagnostic.transform(corr_results)
 
-            for diagnostic in diagnostics:
-                diagnostic.target_image = img_key
-                contribution_table, cluster_df, _ = diagnostic.transform(corr_results)
-
-                diag_name = diagnostic.__class__.__name__
-                clust_tbl_name = f"cluster_{img_name}"
-                diag_tbl_name = f"{diag_name}_{img_name}"
-                if not contribution_table.empty:
-                    corr_results.tables[clust_tbl_name] = cluster_df
-                    corr_results.tables[diag_tbl_name] = contribution_table
-                else:
-                    LGR.warn(
-                        f"Key {diag_tbl_name} and {clust_tbl_name} will not be stored in "
-                        "MetaResult.tables dictionary."
-                    )
+        diag_name = diagnostic.__class__.__name__
+        clust_tbl_name = f"{img_key}_clust"
+        count_tbl_name = f"{img_key}_{diag_name}"
+        if not contribution_table.empty:
+            corr_results.tables[clust_tbl_name] = clusters_table
+            corr_results.tables[count_tbl_name] = contribution_table
+        else:
+            LGR.warn(
+                f"Key {count_tbl_name} and {clust_tbl_name} will not be stored in "
+                "MetaResult.tables dictionary."
+            )
 
     if output_dir is not None:
-        LGR.info(f"Saving meta-analytic maps and tables result to {output_dir}...")
+        LGR.info(f"Saving meta-analytic maps, tables and boilerplate to {output_dir}...")
         corr_results.save_maps(output_dir=output_dir)
         corr_results.save_tables(output_dir=output_dir)
 
+        boilerplate = corr_results.description_
+        with open(op.join(output_dir, "boilerplate.txt"), "w") as fo:
+            fo.write(boilerplate)
+
+        bibtex = corr_results.bibtex_
+        with open(op.join(output_dir, "references.bib"), "w") as fo:
+            fo.write(bibtex)
+
+    LGR.info("Workflow completed.")
     return corr_results

From e35143f7c437cd6a52815211f1c0e02afe0b583c Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 13:03:57 -0400
Subject: [PATCH 06/32] Update cbma.py

---
 nimare/workflows/cbma.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 5acfbdaf3..dd1703938 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -12,7 +12,7 @@
 
 def cbma_workflow(
     dataset,
-    meta_estimator=ALE(null_method="approximate"),
+    meta_estimator=ALE(),
     corrector=FWECorrector(),
     diagnostics=(Jackknife(),),
     output_dir=None,

From cd1df83354ebbf2c4d6762547bf87feb25f68e30 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 15:39:01 -0400
Subject: [PATCH 07/32] support string inputs

---
 nimare/tests/test_workflows.py | 12 +++---
 nimare/workflows/cbma.py       | 68 ++++++++++++++++++++++++++++++----
 2 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 65cb4d7fa..21f5336a2 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -106,12 +106,12 @@ def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
 
     assert isinstance(cres, nimare.results.MetaResult)
 
-    assert "cluster_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "cluster_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "cluster_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "Jackknife_desc-mass_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "Jackknife_desc-size_level-cluster_corr-FWE_method-montecarlo" in cres.tables.keys()
-    assert "Jackknife_level-voxel_corr-FWE_method-montecarlo" in cres.tables.keys()
+    assert "z_desc-mass_level-cluster_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
+    assert "z_desc-size_level-cluster_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
+    assert "z_level-voxel_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
+    assert "z_desc-mass_level-cluster_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
+    assert "z_desc-size_level-cluster_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
+    assert "z_level-voxel_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
 
     for imgtype in cres.maps.keys():
         filename = imgtype + ".nii.gz"
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index dd1703938..34f980198 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -1,18 +1,22 @@
 """Workflow for running an coordinates-based meta-analysis from a NiMARE database."""
+import inspect
 import itertools
 import logging
 import os.path as op
 
-from nimare.correct import FWECorrector
-from nimare.diagnostics import Jackknife
+from nimare.correct import Corrector, FWECorrector
+from nimare.dataset import Dataset
+from nimare.diagnostics import Diagnostics, Jackknife
 from nimare.meta import ALE
+from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare.utils import _check_type
 
 LGR = logging.getLogger(__name__)
 
 
 def cbma_workflow(
     dataset,
-    meta_estimator=ALE(),
+    estimator=None,
     corrector=FWECorrector(),
     diagnostics=(Jackknife(),),
     output_dir=None,
@@ -28,11 +32,13 @@ def cbma_workflow(
     ----------
     dataset : :obj:`~nimare.dataset.Dataset`
         Dataset for which to run meta-analyses to generate maps.
-    meta_estimator : :class:`~nimare.base.CBMAEstimator`, optional
+    estimator : :class:`~nimare.base.CBMAEstimator`, :obj:`str` {'ale', 'scale', 'mkdadensity',
+    'kda'}, or optional
         Meta-analysis estimator. Default is :class:`~nimare.meta.cbma.ale.ALE`.
-    meta_corrector : :class:`~nimare.correct.Corrector`, optional
+    corrector : :class:`~nimare.correct.Corrector`, :obj:`str` {'montecarlo', 'fdr', 'bonferroni'}
+    or optional
         Meta-analysis corrector. Default is :class:`~nimare.correct.FWECorrector`.
-    diagnostics : :obj:`tuple`, optional
+    diagnostics : :obj:`tuple`, :obj:`str` {'jackknife', 'focusCounter'}, or optional
         Tuple of meta-analysis diagnostic classes.
         Default is :class:`~nimare.diagnostics.FocusCounter`.
     output_dir : :obj:`str`, optional
@@ -44,8 +50,56 @@ def cbma_workflow(
     :obj:`~nimare.results.MetaResult`
         Results of Estimator and Corrector fitting with cluster and diagnostic tables.
     """
+    # Check dataset type
+    dataset = _check_type(dataset, Dataset)
+
+    # Options allows for string input
+    estm_options = ("ale", "scale", "mkdadensity", "kda")
+    corr_options = ("montecarlo", "fdr", "bonferroni")
+    diag_options = ("jackknife", "focuscounter")
+
+    # Check estimator type
+    if estimator is None:
+        estimator = ALE()
+    elif inspect.isclass(estimator):
+        estimator = _check_type(estimator, CBMAEstimator)
+    elif isinstance(estimator, str):
+        if estimator not in estm_options:
+            raise ValueError(f'"estimator" of kind string must be {", ".join(estm_options)}')
+    else:
+        raise ValueError(
+            f'"estimator" is {type(estimator)}, it must be a kind of CBMAEstimator, or a string.'
+        )
+
+    # Check corrector type
+    if inspect.isclass(corrector):
+        corrector = _check_type(corrector, Corrector)
+    elif isinstance(corrector, str):
+        if corrector not in corr_options:
+            raise ValueError(f'"corrector" of kind string must be {", ".join(corr_options)}')
+    else:
+        raise ValueError(
+            f'"corrector" is {type(corrector)}, it must be a kind of Corrector, or a string.'
+        )
+
+    # Check diagnostics type
+    if inspect.isclass(diagnostics):
+        diagnostics = _check_type(diagnostics, Diagnostics)
+    elif isinstance(diagnostics, str):
+        if diagnostics not in diag_options:
+            raise ValueError(f'"diagnostics" of kind string must be {", ".join(diag_options)}')
+    else:
+        raise ValueError(
+            f'"diagnostics" is {type(diagnostics)}, it must be a kind of Diagnostics, or a string.'
+        )
+
+    if isinstance(estimator, PairwiseCBMAEstimator):
+        raise AttributeError(
+            "The cbma_workflow function does not currently work with pairwise Estimators."
+        )
+
     LGR.info("Performing meta-analysis...")
-    results = meta_estimator.fit(dataset)
+    results = estimator.fit(dataset)
 
     LGR.info("Performing correction on meta-analysis...")
     corr_results = corrector.transform(results)

From 9649f049e4534a1a7c3f12fa0ff47f7a1440be06 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 16:04:17 -0400
Subject: [PATCH 08/32] refactor code

---
 nimare/workflows/cbma.py | 67 +++++++++++++++++++---------------------
 1 file changed, 31 insertions(+), 36 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 34f980198..b9df7fb7e 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -14,11 +14,28 @@
 LGR = logging.getLogger(__name__)
 
 
+def _collect_class(obj, clss):
+    """Collect a class from a module."""
+    pass
+
+
+def _check_input(obj, clss, options):
+    if inspect.isclass(obj):
+        obj = _check_type(obj, clss)
+    elif isinstance(obj, str):
+        if obj not in options:
+            raise ValueError(f'"estimator" of kind string must be {", ".join(options)}')
+        obj = _collect_class(obj, clss)
+    else:
+        raise ValueError(f'"estimator" is {type(obj)}, it must be a kind of {clss}, or a string.')
+    return obj
+
+
 def cbma_workflow(
     dataset,
     estimator=None,
-    corrector=FWECorrector(),
-    diagnostics=(Jackknife(),),
+    corrector=None,
+    diagnostics=None,
     output_dir=None,
 ):
     """Compose a coordinate-based meta-analysis workflow.
@@ -58,40 +75,18 @@ def cbma_workflow(
     corr_options = ("montecarlo", "fdr", "bonferroni")
     diag_options = ("jackknife", "focuscounter")
 
-    # Check estimator type
-    if estimator is None:
-        estimator = ALE()
-    elif inspect.isclass(estimator):
-        estimator = _check_type(estimator, CBMAEstimator)
-    elif isinstance(estimator, str):
-        if estimator not in estm_options:
-            raise ValueError(f'"estimator" of kind string must be {", ".join(estm_options)}')
-    else:
-        raise ValueError(
-            f'"estimator" is {type(estimator)}, it must be a kind of CBMAEstimator, or a string.'
-        )
-
-    # Check corrector type
-    if inspect.isclass(corrector):
-        corrector = _check_type(corrector, Corrector)
-    elif isinstance(corrector, str):
-        if corrector not in corr_options:
-            raise ValueError(f'"corrector" of kind string must be {", ".join(corr_options)}')
-    else:
-        raise ValueError(
-            f'"corrector" is {type(corrector)}, it must be a kind of Corrector, or a string.'
-        )
-
-    # Check diagnostics type
-    if inspect.isclass(diagnostics):
-        diagnostics = _check_type(diagnostics, Diagnostics)
-    elif isinstance(diagnostics, str):
-        if diagnostics not in diag_options:
-            raise ValueError(f'"diagnostics" of kind string must be {", ".join(diag_options)}')
-    else:
-        raise ValueError(
-            f'"diagnostics" is {type(diagnostics)}, it must be a kind of Diagnostics, or a string.'
-        )
+    # Check inputs and set defaults
+    estimator = (
+        ALE() if corrector is None else _check_input(corrector, CBMAEstimator, estm_options)
+    )
+    corrector = (
+        FWECorrector() if corrector is None else _check_input(corrector, Corrector, corr_options)
+    )
+    diagnostics = (
+        (Jackknife(),)
+        if diagnostics is None
+        else _check_input(diagnostics, Diagnostics, diag_options)
+    )
 
     if isinstance(estimator, PairwiseCBMAEstimator):
         raise AttributeError(

From 1652329edded85e56c95acafeb663520a8d4e8bb Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 16:10:01 -0400
Subject: [PATCH 09/32] Update cbma.py

---
 nimare/workflows/cbma.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index b9df7fb7e..c3722fa8e 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -14,7 +14,7 @@
 LGR = logging.getLogger(__name__)
 
 
-def _collect_class(obj, clss):
+def _collect_class(str_name, base_clss):
     """Collect a class from a module."""
     pass
 
@@ -77,7 +77,7 @@ def cbma_workflow(
 
     # Check inputs and set defaults
     estimator = (
-        ALE() if corrector is None else _check_input(corrector, CBMAEstimator, estm_options)
+        ALE() if estimator is None else _check_input(estimator, CBMAEstimator, estm_options)
     )
     corrector = (
         FWECorrector() if corrector is None else _check_input(corrector, Corrector, corr_options)

From 1c6a268c329afdd0c03bcb2c5691d99ce60ed851 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 17:23:31 -0400
Subject: [PATCH 10/32] [skip CI] support n_cores

---
 nimare/workflows/cbma.py | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index c3722fa8e..7fb1319d1 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -9,7 +9,7 @@
 from nimare.diagnostics import Diagnostics, Jackknife
 from nimare.meta import ALE
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
-from nimare.utils import _check_type
+from nimare.utils import _check_ncores, _check_type
 
 LGR = logging.getLogger(__name__)
 
@@ -19,13 +19,13 @@ def _collect_class(str_name, base_clss):
     pass
 
 
-def _check_input(obj, clss, options):
+def _check_input(obj, clss, options, **kwargs):
     if inspect.isclass(obj):
-        obj = _check_type(obj, clss)
+        obj = _check_type(obj, clss, **kwargs)
     elif isinstance(obj, str):
         if obj not in options:
             raise ValueError(f'"estimator" of kind string must be {", ".join(options)}')
-        obj = _collect_class(obj, clss)
+        obj = _collect_class(obj, clss, **kwargs)
     else:
         raise ValueError(f'"estimator" is {type(obj)}, it must be a kind of {clss}, or a string.')
     return obj
@@ -37,6 +37,7 @@ def cbma_workflow(
     corrector=None,
     diagnostics=None,
     output_dir=None,
+    n_cores=1,
 ):
     """Compose a coordinate-based meta-analysis workflow.
 
@@ -61,12 +62,18 @@ def cbma_workflow(
     output_dir : :obj:`str`, optional
         Output directory in which to save results. If the directory doesn't
         exist, it will be created. Default is None (the results are not saved).
+    n_cores : :obj:`int`, optional
+        Number of cores to use for parallelization.
+        If <=0, defaults to using all available cores.
+        Default is 1.
 
     Returns
     -------
     :obj:`~nimare.results.MetaResult`
         Results of Estimator and Corrector fitting with cluster and diagnostic tables.
     """
+    n_cores = _check_ncores(n_cores)
+
     # Check dataset type
     dataset = _check_type(dataset, Dataset)
 
@@ -75,22 +82,26 @@ def cbma_workflow(
     corr_options = ("montecarlo", "fdr", "bonferroni")
     diag_options = ("jackknife", "focuscounter")
 
-    # Check inputs and set defaults
+    # Check inputs and set defaults if input is None
     estimator = (
-        ALE() if estimator is None else _check_input(estimator, CBMAEstimator, estm_options)
+        ALE(n_cores=n_cores)
+        if estimator is None
+        else _check_input(estimator, CBMAEstimator, estm_options, n_cores=n_cores)
     )
     corrector = (
-        FWECorrector() if corrector is None else _check_input(corrector, Corrector, corr_options)
+        FWECorrector(method="montecarlo", n_cores=n_cores)
+        if corrector is None
+        else _check_input(corrector, Corrector, corr_options, n_cores=n_cores)
     )
     diagnostics = (
-        (Jackknife(),)
+        (Jackknife(n_cores=n_cores),)
         if diagnostics is None
-        else _check_input(diagnostics, Diagnostics, diag_options)
+        else _check_input(diagnostics, Diagnostics, diag_options, n_cores=n_cores)
     )
 
     if isinstance(estimator, PairwiseCBMAEstimator):
         raise AttributeError(
-            "The cbma_workflow function does not currently work with pairwise Estimators."
+            'The "cbma_workflow" function does not currently work with pairwise Estimators.'
         )
 
     LGR.info("Performing meta-analysis...")

From 5d24099f09972094f9630b6f971bc6c3b7f77901 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 21:06:39 -0400
Subject: [PATCH 11/32] [skip ci] map string to classes

---
 nimare/tests/test_workflows.py |  9 +++----
 nimare/workflows/cbma.py       | 44 +++++++++++++++++++++++-----------
 2 files changed, 35 insertions(+), 18 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 21f5336a2..c80cdb1ae 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -92,13 +92,14 @@ def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
     tmpdir = tmp_path_factory.mktemp("test_cbma_workflow_function_smoke")
 
     # Initialize estimator, corrector and diagnostic classes
-    est = ALE(null_method="approximate")
-    corr = FWECorrector(method="montecarlo", n_iters=100)
-    diag = Jackknife()
+    est = ALE
+    # corr = FWECorrector(method="montecarlo", n_iters=100)
+    corr = "montecarlo"
+    diag = Jackknife
 
     cres = workflows.cbma_workflow(
         testdata_cbma_full,
-        meta_estimator=est,
+        estimator=est,
         corrector=corr,
         diagnostics=(diag,),
         output_dir=tmpdir,
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 7fb1319d1..dc4246eee 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -4,31 +4,47 @@
 import logging
 import os.path as op
 
-from nimare.correct import Corrector, FWECorrector
+from nimare.correct import Corrector, FDRCorrector, FWECorrector
 from nimare.dataset import Dataset
-from nimare.diagnostics import Diagnostics, Jackknife
-from nimare.meta import ALE
+from nimare.diagnostics import FocusCounter, Jackknife
+from nimare.meta import ALE, KDA, SCALE, MKDADensity
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
 from nimare.utils import _check_ncores, _check_type
 
 LGR = logging.getLogger(__name__)
 
 
-def _collect_class(str_name, base_clss):
-    """Collect a class from a module."""
-    pass
+def _str_to_class(str_name):
+    """Match a string to a class name without initializing the class."""
+    classes = {
+        "ale": ALE,
+        "scale": SCALE,
+        "mkdadensity": MKDADensity,
+        "kda": KDA,
+        "montecarlo": FWECorrector,
+        "fdr": FDRCorrector,
+        "bonferroni": FWECorrector,
+        "jackknife": Jackknife,
+        "focuscounter": FocusCounter,
+    }
+    return classes[str_name]
 
 
 def _check_input(obj, clss, options, **kwargs):
-    if inspect.isclass(obj):
-        obj = _check_type(obj, clss, **kwargs)
-    elif isinstance(obj, str):
+    """Check input for workflow functions."""
+    if isinstance(obj, str):
         if obj not in options:
             raise ValueError(f'"estimator" of kind string must be {", ".join(options)}')
-        obj = _collect_class(obj, clss, **kwargs)
-    else:
-        raise ValueError(f'"estimator" is {type(obj)}, it must be a kind of {clss}, or a string.')
-    return obj
+
+        # Get the class from the string
+        obj_str = obj
+        obj = _str_to_class(obj_str)
+
+        # Add the method to the kwargs if it's a FWECorrector
+        if obj == FWECorrector:
+            kwargs["method"] = obj_str
+
+    return _check_type(obj, clss, **kwargs)
 
 
 def cbma_workflow(
@@ -96,7 +112,7 @@ def cbma_workflow(
     diagnostics = (
         (Jackknife(n_cores=n_cores),)
         if diagnostics is None
-        else _check_input(diagnostics, Diagnostics, diag_options, n_cores=n_cores)
+        else _check_input(diagnostics, Jackknife, diag_options, n_cores=n_cores)
     )
 
     if isinstance(estimator, PairwiseCBMAEstimator):

From 81ea6b35f7fa42a2641aa6ad04c855551801fcdd Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 22:00:13 -0400
Subject: [PATCH 12/32] [skip ci] test possible combinations

---
 nimare/tests/test_workflows.py | 55 ++++++++++++++++++++--------------
 1 file changed, 32 insertions(+), 23 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index c80cdb1ae..056e046f9 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -1,11 +1,13 @@
 """Test nimare.workflows."""
 import os.path as op
 
+import pytest
+
 import nimare
 from nimare import cli, workflows
 from nimare.correct import FWECorrector
-from nimare.diagnostics import Jackknife
-from nimare.meta.cbma.ale import ALE
+from nimare.diagnostics import FocusCounter, Jackknife
+from nimare.meta.cbma import ALE, MKDAChi2
 from nimare.tests.utils import get_test_data_path
 
 
@@ -87,33 +89,40 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
     assert op.isfile(op.join(tmpdir, f"{prefix}_group2_input_coordinates.txt"))
 
 
-def test_cbma_workflow_function_smoke(tmp_path_factory, testdata_cbma_full):
+@pytest.mark.parametrize(
+    "estimator,corrector,diagnostics",
+    [
+        (ALE, FWECorrector(method="montecarlo", n_iters=100), [Jackknife]),
+        ("ale" "bonferroni", [Jackknife, FocusCounter]),
+        ("kda", "fdr", Jackknife),
+        (MKDAChi2, "montecarlo", "focusCounter"),
+    ],
+)
+def test_cbma_workflow_function_smoke(
+    tmp_path_factory, testdata_cbma_full, estimator, corrector, diagnostics
+):
     """Run smoke test for CBMA workflow."""
     tmpdir = tmp_path_factory.mktemp("test_cbma_workflow_function_smoke")
 
-    # Initialize estimator, corrector and diagnostic classes
-    est = ALE
-    # corr = FWECorrector(method="montecarlo", n_iters=100)
-    corr = "montecarlo"
-    diag = Jackknife
-
-    cres = workflows.cbma_workflow(
-        testdata_cbma_full,
-        estimator=est,
-        corrector=corr,
-        diagnostics=(diag,),
-        output_dir=tmpdir,
-    )
+    if estimator == MKDAChi2:
+        with pytest.raises(AttributeError):
+            workflows.cbma_workflow(
+                testdata_cbma_full,
+                estimator=estimator,
+                corrector=corrector,
+                diagnostics=diagnostics,
+            )
+    else:
+        cres = workflows.cbma_workflow(
+            testdata_cbma_full,
+            estimator=estimator,
+            corrector=corrector,
+            diagnostics=diagnostics,
+            output_dir=tmpdir,
+        )
 
     assert isinstance(cres, nimare.results.MetaResult)
 
-    assert "z_desc-mass_level-cluster_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
-    assert "z_desc-size_level-cluster_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
-    assert "z_level-voxel_corr-FWE_method-montecarlo_clust" in cres.tables.keys()
-    assert "z_desc-mass_level-cluster_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
-    assert "z_desc-size_level-cluster_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
-    assert "z_level-voxel_corr-FWE_method-montecarlo_Jackknife" in cres.tables.keys()
-
     for imgtype in cres.maps.keys():
         filename = imgtype + ".nii.gz"
         outpath = op.join(tmpdir, filename)

From d3a878bc2e065e313221bc67cae7f94c7aba99ee Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Thu, 16 Mar 2023 22:05:39 -0400
Subject: [PATCH 13/32] [skip CI] Also support single diagnostic class

---
 nimare/workflows/cbma.py | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index dc4246eee..bb2854e6e 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -1,12 +1,11 @@
 """Workflow for running an coordinates-based meta-analysis from a NiMARE database."""
-import inspect
 import itertools
 import logging
 import os.path as op
 
 from nimare.correct import Corrector, FDRCorrector, FWECorrector
 from nimare.dataset import Dataset
-from nimare.diagnostics import FocusCounter, Jackknife
+from nimare.diagnostics import Diagnostics, FocusCounter, Jackknife
 from nimare.meta import ALE, KDA, SCALE, MKDADensity
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
 from nimare.utils import _check_ncores, _check_type
@@ -72,8 +71,9 @@ def cbma_workflow(
     corrector : :class:`~nimare.correct.Corrector`, :obj:`str` {'montecarlo', 'fdr', 'bonferroni'}
     or optional
         Meta-analysis corrector. Default is :class:`~nimare.correct.FWECorrector`.
-    diagnostics : :obj:`tuple`, :obj:`str` {'jackknife', 'focusCounter'}, or optional
-        Tuple of meta-analysis diagnostic classes.
+    diagnostics : :obj:`list` of :class:`~nimare.diagnostics.Diagnostics`,
+    :class:`~nimare.diagnostics.Diagnostics`, :obj:`str` {'jackknife', 'focusCounter'}, or optional
+        List of meta-analysis diagnostic classes. A single diagnostic class can also be passed.
         Default is :class:`~nimare.diagnostics.FocusCounter`.
     output_dir : :obj:`str`, optional
         Output directory in which to save results. If the directory doesn't
@@ -81,6 +81,8 @@ def cbma_workflow(
     n_cores : :obj:`int`, optional
         Number of cores to use for parallelization.
         If <=0, defaults to using all available cores.
+        If estimator, corrector, or diagnostics are passed as initialized objects, this parameter
+        will be ignored.
         Default is 1.
 
     Returns
@@ -90,6 +92,9 @@ def cbma_workflow(
     """
     n_cores = _check_ncores(n_cores)
 
+    if not isinstance(diagnostics, list) and diagnostics is not None:
+        diagnostics = [diagnostics]
+
     # Check dataset type
     dataset = _check_type(dataset, Dataset)
 
@@ -109,11 +114,14 @@ def cbma_workflow(
         if corrector is None
         else _check_input(corrector, Corrector, corr_options, n_cores=n_cores)
     )
-    diagnostics = (
-        (Jackknife(n_cores=n_cores),)
-        if diagnostics is None
-        else _check_input(diagnostics, Jackknife, diag_options, n_cores=n_cores)
-    )
+
+    if diagnostics is None:
+        diagnostics = [FocusCounter(n_cores=n_cores)]
+    else:
+        diagnostics = [
+            _check_input(diagnostic, Diagnostics, diag_options, n_cores=n_cores)
+            for diagnostic in diagnostics
+        ]
 
     if isinstance(estimator, PairwiseCBMAEstimator):
         raise AttributeError(

From 4615ebf156a7222668954036fe0611e8c057000f Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 10:43:36 -0400
Subject: [PATCH 14/32] Use FDR in the example

---
 .../02_meta-analyses/10_plot_cbma_workflow.py     | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/examples/02_meta-analyses/10_plot_cbma_workflow.py b/examples/02_meta-analyses/10_plot_cbma_workflow.py
index b8626c375..e696bdb4c 100644
--- a/examples/02_meta-analyses/10_plot_cbma_workflow.py
+++ b/examples/02_meta-analyses/10_plot_cbma_workflow.py
@@ -34,12 +34,15 @@
 # The CBMA workflow function runs the following steps:
 #
 # 1. Runs a meta-analysis using the specified method (default: ALE)
-# 2. Applies a corrector to the meta-analysis results (default: FWECorrector)
+# 2. Applies a corrector to the meta-analysis results (default: FWECorrector, montecarlo)
 # 3. Generates cluster tables and runs diagnostics on the corrected results (default: Jackknife)
 #
 # All in one function call!
-
-result = cbma_workflow(dset)
+# result = cbma_workflow(dset)
+# For this example, we use an FDR correction because the default corrector (FWE correction with
+# Monte Carlo simulation) takes a long time to run due to the high number of iterations that
+# are required
+result = cbma_workflow(dset, corrector="fdr")
 
 ###############################################################################
 # Plot Results
@@ -48,7 +51,7 @@
 # where you can access the corrected results of the meta-analysis and diagnostics tables.
 #
 # Corrected map:
-img = result.get_map("z_corr-FWE_method-bonferroni")
+img = result.get_map("z_corr-FDR")
 plot_stat_map(
     img,
     cut_coords=4,
@@ -62,12 +65,12 @@
 ###############################################################################
 # Clusters table
 # ``````````````````````````````````````````````````````````````````````````````
-result.tables["z_corr-FWE_method-bonferroni_clust"]
+result.tables["z_corr-FDR_clust"]
 
 ###############################################################################
 # Contribution table
 # ``````````````````````````````````````````````````````````````````````````````
-result.tables["z_corr-FWE_method-bonferroni_Jackknife"]
+result.tables["z_corr-FDR_Jackknife"]
 
 ###############################################################################
 # Methods

From 373fd2295eb23b46f410d072d30ae6f9ed1391e7 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 14:41:25 -0400
Subject: [PATCH 15/32] Update test_workflows.py

---
 nimare/tests/test_workflows.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 056e046f9..b70b66916 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -122,6 +122,8 @@ def test_cbma_workflow_function_smoke(
         )
 
     assert isinstance(cres, nimare.results.MetaResult)
+    assert op.isfile(op.join(tmpdir, "boilerplate.txt"))
+    assert op.isfile(op.join(tmpdir, "references.bib"))
 
     for imgtype in cres.maps.keys():
         filename = imgtype + ".nii.gz"

From 6317595a9e4d1eed14cd9929db06b06752f1d258 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 14:47:46 -0400
Subject: [PATCH 16/32] Update test_workflows.py

---
 nimare/tests/test_workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index b70b66916..01cdc4ea5 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -93,7 +93,7 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
     "estimator,corrector,diagnostics",
     [
         (ALE, FWECorrector(method="montecarlo", n_iters=100), [Jackknife]),
-        ("ale" "bonferroni", [Jackknife, FocusCounter]),
+        ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
         (MKDAChi2, "montecarlo", "focusCounter"),
     ],

From 5318cca9b1955fef3e3b0eaea8f059b1fc0b4e88 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 15:00:13 -0400
Subject: [PATCH 17/32] fix tests

---
 nimare/tests/test_workflows.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 01cdc4ea5..de3ab20d6 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -95,7 +95,7 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
         (ALE, FWECorrector(method="montecarlo", n_iters=100), [Jackknife]),
         ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
-        (MKDAChi2, "montecarlo", "focusCounter"),
+        (MKDAChi2, "montecarlo", "focuscounter"),
     ],
 )
 def test_cbma_workflow_function_smoke(
@@ -121,16 +121,16 @@ def test_cbma_workflow_function_smoke(
             output_dir=tmpdir,
         )
 
-    assert isinstance(cres, nimare.results.MetaResult)
-    assert op.isfile(op.join(tmpdir, "boilerplate.txt"))
-    assert op.isfile(op.join(tmpdir, "references.bib"))
+        assert isinstance(cres, nimare.results.MetaResult)
+        assert op.isfile(op.join(tmpdir, "boilerplate.txt"))
+        assert op.isfile(op.join(tmpdir, "references.bib"))
 
-    for imgtype in cres.maps.keys():
-        filename = imgtype + ".nii.gz"
-        outpath = op.join(tmpdir, filename)
-        assert op.isfile(outpath)
+        for imgtype in cres.maps.keys():
+            filename = imgtype + ".nii.gz"
+            outpath = op.join(tmpdir, filename)
+            assert op.isfile(outpath)
 
-    for tabletype in cres.tables.keys():
-        filename = tabletype + ".tsv"
-        outpath = op.join(tmpdir, filename)
-        assert op.isfile(outpath)
+        for tabletype in cres.tables.keys():
+            filename = tabletype + ".tsv"
+            outpath = op.join(tmpdir, filename)
+            assert op.isfile(outpath)

From 51bbef13328f1a5c574b3c4cf98438c38de36440 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 15:00:41 -0400
Subject: [PATCH 18/32] Update test_workflows.py

---
 nimare/tests/test_workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index de3ab20d6..241ecdf7f 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -92,7 +92,7 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
 @pytest.mark.parametrize(
     "estimator,corrector,diagnostics",
     [
-        (ALE, FWECorrector(method="montecarlo", n_iters=100), [Jackknife]),
+        (ALE, FWECorrector(method="montecarlo", n_iters=10), [Jackknife]),
         ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
         (MKDAChi2, "montecarlo", "focuscounter"),

From 5fa9327b7b693c38050690c80c4bcc4f6c1ef2bc Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 15:05:49 -0400
Subject: [PATCH 19/32] Use warning instead of warn

---
 nimare/workflows/cbma.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index bb2854e6e..7c2979829 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -151,7 +151,7 @@ def cbma_workflow(
             corr_results.tables[clust_tbl_name] = clusters_table
             corr_results.tables[count_tbl_name] = contribution_table
         else:
-            LGR.warn(
+            LGR.warning(
                 f"Key {count_tbl_name} and {clust_tbl_name} will not be stored in "
                 "MetaResult.tables dictionary."
             )

From dd5246137712f56838174749092a2f4adbeeca3b Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 16:03:37 -0400
Subject: [PATCH 20/32] Set default voxel_thresh for diagnostics

---
 examples/02_meta-analyses/10_plot_cbma_workflow.py | 8 ++++----
 nimare/workflows/cbma.py                           | 7 +++++--
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/examples/02_meta-analyses/10_plot_cbma_workflow.py b/examples/02_meta-analyses/10_plot_cbma_workflow.py
index e696bdb4c..a85ffbcb5 100644
--- a/examples/02_meta-analyses/10_plot_cbma_workflow.py
+++ b/examples/02_meta-analyses/10_plot_cbma_workflow.py
@@ -51,12 +51,12 @@
 # where you can access the corrected results of the meta-analysis and diagnostics tables.
 #
 # Corrected map:
-img = result.get_map("z_corr-FDR")
+img = result.get_map("z_corr-FDR_method-indep")
 plot_stat_map(
     img,
     cut_coords=4,
     display_mode="z",
-    threshold=2.326,  # cluster-level p < .01, one-tailed
+    threshold=3.1,  # cluster-level p < 0.001, one-tailed
     cmap="RdBu_r",
     vmax=4,
 )
@@ -65,12 +65,12 @@
 ###############################################################################
 # Clusters table
 # ``````````````````````````````````````````````````````````````````````````````
-result.tables["z_corr-FDR_clust"]
+result.tables["z_corr-FDR_method-indep_clust"]
 
 ###############################################################################
 # Contribution table
 # ``````````````````````````````````````````````````````````````````````````````
-result.tables["z_corr-FDR_Jackknife"]
+result.tables["z_corr-FDR_method-indep_Jackknife"]
 
 ###############################################################################
 # Methods
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 7c2979829..10bc3d7ac 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -8,6 +8,7 @@
 from nimare.diagnostics import Diagnostics, FocusCounter, Jackknife
 from nimare.meta import ALE, KDA, SCALE, MKDADensity
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare.transforms import p_to_z
 from nimare.utils import _check_ncores, _check_type
 
 LGR = logging.getLogger(__name__)
@@ -115,11 +116,13 @@ def cbma_workflow(
         else _check_input(corrector, Corrector, corr_options, n_cores=n_cores)
     )
 
+    pval = 0.05 if corrector.method == "montecarlo" else 0.001
+    vthr = p_to_z(pval, tail="one")  # Set voxel_thresh for diagnostics
     if diagnostics is None:
-        diagnostics = [FocusCounter(n_cores=n_cores)]
+        diagnostics = [Jackknife(voxel_thresh=vthr, n_cores=n_cores)]
     else:
         diagnostics = [
-            _check_input(diagnostic, Diagnostics, diag_options, n_cores=n_cores)
+            _check_input(diagnostic, Diagnostics, diag_options, voxel_thresh=vthr, n_cores=n_cores)
             for diagnostic in diagnostics
         ]
 

From 6e74b0cb3d616c1baa85f8e16eae64220014b61c Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 16:15:04 -0400
Subject: [PATCH 21/32] Update diagnostics.py

---
 nimare/diagnostics.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/diagnostics.py b/nimare/diagnostics.py
index af421c8ec..583c549b9 100644
--- a/nimare/diagnostics.py
+++ b/nimare/diagnostics.py
@@ -73,7 +73,7 @@ def transform(self, result):
         """
         none_contribution_table = False
         if not hasattr(result.estimator, "dataset"):
-            LGR.warn(
+            LGR.warning(
                 "MetaResult was not generated by an Estimator with a `dataset` attribute. "
                 "This may be because the Estimator was a pairwise Estimator. The "
                 "Jackknife/FocusCounter method does not currently work with pairwise Estimators. "

From b004ef4fc4bc2128acd8799fe49fcfcaae309637 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Fri, 17 Mar 2023 16:45:52 -0400
Subject: [PATCH 22/32] update doc, fix typo

---
 examples/02_meta-analyses/10_plot_cbma_workflow.py |  2 ++
 nimare/workflows/cbma.py                           | 13 +++++++------
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/examples/02_meta-analyses/10_plot_cbma_workflow.py b/examples/02_meta-analyses/10_plot_cbma_workflow.py
index a85ffbcb5..bf02fb3a7 100644
--- a/examples/02_meta-analyses/10_plot_cbma_workflow.py
+++ b/examples/02_meta-analyses/10_plot_cbma_workflow.py
@@ -38,7 +38,9 @@
 # 3. Generates cluster tables and runs diagnostics on the corrected results (default: Jackknife)
 #
 # All in one function call!
+#
 # result = cbma_workflow(dset)
+#
 # For this example, we use an FDR correction because the default corrector (FWE correction with
 # Monte Carlo simulation) takes a long time to run due to the high number of iterations that
 # are required
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 10bc3d7ac..a25b8d402 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -66,14 +66,15 @@ def cbma_workflow(
     ----------
     dataset : :obj:`~nimare.dataset.Dataset`
         Dataset for which to run meta-analyses to generate maps.
-    estimator : :class:`~nimare.base.CBMAEstimator`, :obj:`str` {'ale', 'scale', 'mkdadensity',
+    estimator : :class:`~nimare.base.CBMAEstimator`, :obj:`str` {'ale', 'scale', 'mkdadensity', \
     'kda'}, or optional
         Meta-analysis estimator. Default is :class:`~nimare.meta.cbma.ale.ALE`.
-    corrector : :class:`~nimare.correct.Corrector`, :obj:`str` {'montecarlo', 'fdr', 'bonferroni'}
-    or optional
+    corrector : :class:`~nimare.correct.Corrector`, :obj:`str` {'montecarlo', 'fdr', \
+    'bonferroni'} or optional
         Meta-analysis corrector. Default is :class:`~nimare.correct.FWECorrector`.
-    diagnostics : :obj:`list` of :class:`~nimare.diagnostics.Diagnostics`,
-    :class:`~nimare.diagnostics.Diagnostics`, :obj:`str` {'jackknife', 'focusCounter'}, or optional
+    diagnostics : :obj:`list` of :class:`~nimare.diagnostics.Diagnostics`, \
+    :class:`~nimare.diagnostics.Diagnostics`, :obj:`str` {'jackknife', 'focusCounter'}, \
+    or optional
         List of meta-analysis diagnostic classes. A single diagnostic class can also be passed.
         Default is :class:`~nimare.diagnostics.FocusCounter`.
     output_dir : :obj:`str`, optional
@@ -150,7 +151,7 @@ def cbma_workflow(
         diag_name = diagnostic.__class__.__name__
         clust_tbl_name = f"{img_key}_clust"
         count_tbl_name = f"{img_key}_{diag_name}"
-        if not contribution_table.empty:
+        if not clusters_table.empty:
             corr_results.tables[clust_tbl_name] = clusters_table
             corr_results.tables[count_tbl_name] = contribution_table
         else:

From 2c2fddae80e00e644965834ed411ea3f6ce86bc8 Mon Sep 17 00:00:00 2001
From: "Julio A. Peraza" <52050407+JulioAPeraza@users.noreply.github.com>
Date: Sat, 18 Mar 2023 08:59:48 -0400
Subject: [PATCH 23/32] Update nimare/workflows/cbma.py

Co-authored-by: James Kent <jamesdkent21@gmail.com>
---
 nimare/workflows/cbma.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index a25b8d402..29ac8ab2a 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -73,7 +73,7 @@ def cbma_workflow(
     'bonferroni'} or optional
         Meta-analysis corrector. Default is :class:`~nimare.correct.FWECorrector`.
     diagnostics : :obj:`list` of :class:`~nimare.diagnostics.Diagnostics`, \
-    :class:`~nimare.diagnostics.Diagnostics`, :obj:`str` {'jackknife', 'focusCounter'}, \
+    :class:`~nimare.diagnostics.Diagnostics`, :obj:`str` {'jackknife', 'focuscounter'}, \
     or optional
         List of meta-analysis diagnostic classes. A single diagnostic class can also be passed.
         Default is :class:`~nimare.diagnostics.FocusCounter`.

From 244abba535a0e86c8d32d3f6bcb417ee9e5372dc Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 21 Mar 2023 22:07:43 -0400
Subject: [PATCH 24/32] Skips None in save_tables()

---
 nimare/results.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nimare/results.py b/nimare/results.py
index 73841f190..2272c841a 100644
--- a/nimare/results.py
+++ b/nimare/results.py
@@ -179,7 +179,10 @@ def save_tables(self, output_dir=".", prefix="", prefix_sep="_", names=None):
         for tabletype, table in tables.items():
             filename = prefix + tabletype + ".tsv"
             outpath = os.path.join(output_dir, filename)
-            table.to_csv(outpath, sep="\t", index=False)
+            if table is not None:
+                table.to_csv(outpath, sep="\t", index=False)
+            else:
+                LGR.warning(f"Table {tabletype} is None. Not saving.")
 
     def copy(self):
         """Return copy of result object."""

From dd143fc61765ab891b37a2829ea859167cbb9cfb Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 21 Mar 2023 22:08:10 -0400
Subject: [PATCH 25/32] Add empty tables and none to dict too

---
 nimare/workflows/cbma.py | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 29ac8ab2a..fa54bb647 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -8,7 +8,6 @@
 from nimare.diagnostics import Diagnostics, FocusCounter, Jackknife
 from nimare.meta import ALE, KDA, SCALE, MKDADensity
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
-from nimare.transforms import p_to_z
 from nimare.utils import _check_ncores, _check_type
 
 LGR = logging.getLogger(__name__)
@@ -117,13 +116,11 @@ def cbma_workflow(
         else _check_input(corrector, Corrector, corr_options, n_cores=n_cores)
     )
 
-    pval = 0.05 if corrector.method == "montecarlo" else 0.001
-    vthr = p_to_z(pval, tail="one")  # Set voxel_thresh for diagnostics
     if diagnostics is None:
-        diagnostics = [Jackknife(voxel_thresh=vthr, n_cores=n_cores)]
+        diagnostics = [Jackknife(n_cores=n_cores)]
     else:
         diagnostics = [
-            _check_input(diagnostic, Diagnostics, diag_options, voxel_thresh=vthr, n_cores=n_cores)
+            _check_input(diagnostic, Diagnostics, diag_options, n_cores=n_cores)
             for diagnostic in diagnostics
         ]
 
@@ -149,16 +146,8 @@ def cbma_workflow(
         contribution_table, clusters_table, _ = diagnostic.transform(corr_results)
 
         diag_name = diagnostic.__class__.__name__
-        clust_tbl_name = f"{img_key}_clust"
-        count_tbl_name = f"{img_key}_{diag_name}"
-        if not clusters_table.empty:
-            corr_results.tables[clust_tbl_name] = clusters_table
-            corr_results.tables[count_tbl_name] = contribution_table
-        else:
-            LGR.warning(
-                f"Key {count_tbl_name} and {clust_tbl_name} will not be stored in "
-                "MetaResult.tables dictionary."
-            )
+        corr_results.tables[f"{img_key}_clust"] = clusters_table
+        corr_results.tables[f"{img_key}_{diag_name}"] = contribution_table
 
     if output_dir is not None:
         LGR.info(f"Saving meta-analytic maps, tables and boilerplate to {output_dir}...")

From 58d00e74d3b60335dc898ea19dfebb5255497d04 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 19:19:23 -0400
Subject: [PATCH 26/32] Add voxel_thresh and cluster_threshold parameters

---
 nimare/workflows/cbma.py | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index fa54bb647..53a0a198c 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -51,6 +51,8 @@ def cbma_workflow(
     estimator=None,
     corrector=None,
     diagnostics=None,
+    voxel_thresh=1.65,
+    cluster_threshold=10,
     output_dir=None,
     n_cores=1,
 ):
@@ -76,6 +78,19 @@ def cbma_workflow(
     or optional
         List of meta-analysis diagnostic classes. A single diagnostic class can also be passed.
         Default is :class:`~nimare.diagnostics.FocusCounter`.
+    voxel_thresh : :obj:`float` or None, optional
+        An optional voxel-level threshold that may be applied to the ``target_image`` to define
+        clusters. This can be None if the ``target_image`` is already thresholded
+        (e.g., a cluster-level corrected map).
+        If estimator, corrector, or diagnostics are passed as initialized objects, this parameter
+        will be ignored.
+        Default is 1.96, which correspond with `p-value = .05`.
+    cluster_threshold : :obj:`int` or None, optional
+        Cluster size threshold, in :term:`voxels<voxel>`.
+        If None, then no cluster size threshold will be applied.
+        If estimator, corrector, or diagnostics are passed as initialized objects, this parameter
+        will be ignored.
+        Default is 10.
     output_dir : :obj:`str`, optional
         Output directory in which to save results. If the directory doesn't
         exist, it will be created. Default is None (the results are not saved).
@@ -116,11 +131,16 @@ def cbma_workflow(
         else _check_input(corrector, Corrector, corr_options, n_cores=n_cores)
     )
 
+    diag_kwargs = {
+        "voxel_thresh": voxel_thresh,
+        "cluster_threshold": cluster_threshold,
+        "n_cores": n_cores,
+    }
     if diagnostics is None:
-        diagnostics = [Jackknife(n_cores=n_cores)]
+        diagnostics = [Jackknife(**diag_kwargs)]
     else:
         diagnostics = [
-            _check_input(diagnostic, Diagnostics, diag_options, n_cores=n_cores)
+            _check_input(diagnostic, Diagnostics, diag_options, **diag_kwargs)
             for diagnostic in diagnostics
         ]
 

From 60504640f6c828c2fa22c8db843162d8770af028 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 19:19:54 -0400
Subject: [PATCH 27/32] Test non-cbma estimator

---
 nimare/tests/test_workflows.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 241ecdf7f..5f3b46c8d 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -8,6 +8,7 @@
 from nimare.correct import FWECorrector
 from nimare.diagnostics import FocusCounter, Jackknife
 from nimare.meta.cbma import ALE, MKDAChi2
+from nimare.meta.ibma import Fishers
 from nimare.tests.utils import get_test_data_path
 
 
@@ -96,6 +97,7 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
         ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
         (MKDAChi2, "montecarlo", "focuscounter"),
+        (Fishers, "montecarlo", None),
     ],
 )
 def test_cbma_workflow_function_smoke(
@@ -112,6 +114,14 @@ def test_cbma_workflow_function_smoke(
                 corrector=corrector,
                 diagnostics=diagnostics,
             )
+    elif estimator == Fishers:
+        with pytest.raises((AttributeError, ValueError)):
+            workflows.cbma_workflow(
+                testdata_cbma_full,
+                estimator=estimator,
+                corrector=corrector,
+                diagnostics=diagnostics,
+            )
     else:
         cres = workflows.cbma_workflow(
             testdata_cbma_full,
@@ -133,4 +143,6 @@ def test_cbma_workflow_function_smoke(
         for tabletype in cres.tables.keys():
             filename = tabletype + ".tsv"
             outpath = op.join(tmpdir, filename)
-            assert op.isfile(outpath)
+            # For estimator == ALE, tables are None
+            if estimator != ALE:
+                assert op.isfile(outpath)

From 0a817253e36f2586e957ae0de434af11580e0fc5 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 19:19:58 -0400
Subject: [PATCH 28/32] Update base.py

---
 nimare/meta/cbma/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nimare/meta/cbma/base.py b/nimare/meta/cbma/base.py
index 1f738f1ca..61c9b948d 100644
--- a/nimare/meta/cbma/base.py
+++ b/nimare/meta/cbma/base.py
@@ -75,7 +75,7 @@ def __init__(self, kernel_transformer, *, mask=None, **kwargs):
         # Flag any extraneous kwargs
         other_kwargs = dict(set(kwargs.items()) - set(kernel_args.items()))
         if other_kwargs:
-            LGR.warn(f"Unused keyword arguments found: {tuple(other_kwargs.items())}")
+            LGR.warning(f"Unused keyword arguments found: {tuple(other_kwargs.items())}")
 
         # Get kernel transformer
         kernel_args = {k.split("kernel__")[1]: v for k, v in kernel_args.items()}

From 1761655e23b7d362a9acfbdda71894e25c11f8e1 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 19:20:03 -0400
Subject: [PATCH 29/32] Update 10_plot_cbma_workflow.py

---
 examples/02_meta-analyses/10_plot_cbma_workflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/02_meta-analyses/10_plot_cbma_workflow.py b/examples/02_meta-analyses/10_plot_cbma_workflow.py
index bf02fb3a7..ac1aee221 100644
--- a/examples/02_meta-analyses/10_plot_cbma_workflow.py
+++ b/examples/02_meta-analyses/10_plot_cbma_workflow.py
@@ -58,7 +58,7 @@
     img,
     cut_coords=4,
     display_mode="z",
-    threshold=3.1,  # cluster-level p < 0.001, one-tailed
+    threshold=1.65,  # voxel_thresh p < .05, one-tailed
     cmap="RdBu_r",
     vmax=4,
 )

From 050d3a0692d411ab757af1a0caa3e7d5a5b75744 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 19:30:34 -0400
Subject: [PATCH 30/32] Improve coverage

---
 nimare/tests/test_workflows.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index 5f3b46c8d..ce251b6d5 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -96,8 +96,9 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
         (ALE, FWECorrector(method="montecarlo", n_iters=10), [Jackknife]),
         ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
-        (MKDAChi2, "montecarlo", "focuscounter"),
-        (Fishers, "montecarlo", None),
+        ("mkdadensity", "fdr", "focuscounter"),
+        (MKDAChi2, "montecarlo", None),
+        (Fishers, "montecarlo", "jackknife"),
     ],
 )
 def test_cbma_workflow_function_smoke(

From 58f2cfcfa172c2ea8ae6cf21ac3cdb73d2021a94 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 21:21:51 -0400
Subject: [PATCH 31/32] Update documentation

---
 nimare/workflows/cbma.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index 53a0a198c..bad378aba 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -60,8 +60,8 @@ def cbma_workflow(
 
     .. versionadded:: 0.0.14
 
-    This workflow performs a coordinate-based meta-analysis, multiple comparison correction,
-    and diagnostics analyses on corrected meta-analytic maps.
+    This workflow performs a coordinate-based meta-analysis, multiple comparison corrections,
+    and diagnostics analyses on corrected meta-analytic z-score maps.
 
     Parameters
     ----------
@@ -79,17 +79,15 @@ def cbma_workflow(
         List of meta-analysis diagnostic classes. A single diagnostic class can also be passed.
         Default is :class:`~nimare.diagnostics.FocusCounter`.
     voxel_thresh : :obj:`float` or None, optional
-        An optional voxel-level threshold that may be applied to the ``target_image`` to define
-        clusters. This can be None if the ``target_image`` is already thresholded
-        (e.g., a cluster-level corrected map).
-        If estimator, corrector, or diagnostics are passed as initialized objects, this parameter
-        will be ignored.
-        Default is 1.96, which correspond with `p-value = .05`.
+        An optional voxel-level threshold that may be applied to the ``target_image`` in the
+        :class:`~nimare.diagnostics.Diagnostics` class to define clusters. This can be None or 0
+        if the ``target_image`` is already thresholded (e.g., a cluster-level corrected map).
+        If diagnostics are passed as initialized objects, this parameter will be ignored.
+        Default is 1.65, which corresponds to p-value = .05, one-tailed.
     cluster_threshold : :obj:`int` or None, optional
         Cluster size threshold, in :term:`voxels<voxel>`.
         If None, then no cluster size threshold will be applied.
-        If estimator, corrector, or diagnostics are passed as initialized objects, this parameter
-        will be ignored.
+        If diagnostics are passed as initialized objects, this parameter will be ignored.
         Default is 10.
     output_dir : :obj:`str`, optional
         Output directory in which to save results. If the directory doesn't

From 6af419b72ea4007d9a9018ebad3b6861e80e06d1 Mon Sep 17 00:00:00 2001
From: JulioAPeraza <jpera054@fiu.edu>
Date: Tue, 28 Mar 2023 21:25:47 -0400
Subject: [PATCH 32/32] Improve coverage

---
 nimare/tests/test_workflows.py | 9 +++++++++
 nimare/workflows/cbma.py       | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/nimare/tests/test_workflows.py b/nimare/tests/test_workflows.py
index ce251b6d5..518699aed 100644
--- a/nimare/tests/test_workflows.py
+++ b/nimare/tests/test_workflows.py
@@ -94,6 +94,7 @@ def test_ale_workflow_cli_smoke_2(tmp_path_factory):
     "estimator,corrector,diagnostics",
     [
         (ALE, FWECorrector(method="montecarlo", n_iters=10), [Jackknife]),
+        ("ales", "bonferroni", Jackknife),
         ("ale", "bonferroni", [Jackknife, FocusCounter]),
         ("kda", "fdr", Jackknife),
         ("mkdadensity", "fdr", "focuscounter"),
@@ -123,6 +124,14 @@ def test_cbma_workflow_function_smoke(
                 corrector=corrector,
                 diagnostics=diagnostics,
             )
+    elif estimator == "ales":
+        with pytest.raises(ValueError):
+            workflows.cbma_workflow(
+                testdata_cbma_full,
+                estimator=estimator,
+                corrector=corrector,
+                diagnostics=diagnostics,
+            )
     else:
         cres = workflows.cbma_workflow(
             testdata_cbma_full,
diff --git a/nimare/workflows/cbma.py b/nimare/workflows/cbma.py
index bad378aba..7f8e44a8a 100644
--- a/nimare/workflows/cbma.py
+++ b/nimare/workflows/cbma.py
@@ -33,7 +33,7 @@ def _check_input(obj, clss, options, **kwargs):
     """Check input for workflow functions."""
     if isinstance(obj, str):
         if obj not in options:
-            raise ValueError(f'"estimator" of kind string must be {", ".join(options)}')
+            raise ValueError(f'"{obj}" of kind string must be {", ".join(options)}')
 
         # Get the class from the string
         obj_str = obj