[FIX] threshold images right before ploting in GLM reports (#4258)

* fix thresholding in GLM report

* update doc string

* add comment

* fix tests

* fix and pass cut coord to mask

* update changelog

doc/changes/latest.rst

@@ -8,7 +8,8 @@
 Fixes
 -----
 
-- :bdg-dark:`Code` Fix errant warning when using ``stat_type`` in :func:`nilearn.glm.compute_contrast` (:gh:`4257` by `Eric Larson`_)
+- :bdg-dark:`Code` Fix errant warning when using ``stat_type`` in :func:`nilearn.glm.compute_contrast` (:gh:`4257` by `Eric Larson`_).
+- :bdg-dark:`Code` FIX when thresholding is applied to images by GLM reports (:gh:`4258` by `Rémi Gau`_).
 
 Enhancements
 ------------

nilearn/reporting/glm_reporter.py

@@ -224,8 +224,7 @@ def make_glm_report(
             mask_img = model.masker_.mask_img_
 
     mask_plot_html_code = _mask_to_svg(
-        mask_img=mask_img,
-        bg_img=bg_img,
+        mask_img=mask_img, bg_img=bg_img, cut_coords=cut_coords
     )
     all_components = _make_stat_maps_contrast_clusters(
         stat_img=statistical_maps,
@@ -629,7 +628,7 @@ def _resize_plot_inches(plot, width_change=0, height_change=0):
     return plot
 
 
-def _mask_to_svg(mask_img, bg_img):
+def _mask_to_svg(mask_img, bg_img, cut_coords=None):
     """Plot cuts of an mask image and creates SVG code of it.
 
     Parameters
@@ -656,6 +655,7 @@ def _mask_to_svg(mask_img, bg_img):
             bg_img=bg_img,
             display_mode="z",
             cmap="Set1",
+            cut_coords=cut_coords,
         )
         mask_plot_svg = _plot_to_svg(plt.gcf())
         # prevents sphinx-gallery & jupyter from scraping & inserting plots
@@ -763,30 +763,40 @@ def _make_stat_maps_contrast_clusters(
         components_template_text = html_template_obj.read()
     for contrast_name, stat_map_img in stat_img.items():
         component_text_ = string.Template(components_template_text)
-        thresholded_stat_map, threshold = threshold_stats_img(
+
+        # Only use threshold_stats_img to adjust the threshold
+        # that we will pass to  _clustering_params_to_dataframe
+        # and _stat_map_to_svg
+        # Necessary to avoid :
+        # https://github.com/nilearn/nilearn/issues/4192
+        thresholded_img, threshold = threshold_stats_img(
             stat_img=stat_map_img,
             threshold=threshold,
             alpha=alpha,
             cluster_threshold=cluster_threshold,
             height_control=height_control,
         )
+
         table_details = _clustering_params_to_dataframe(
             threshold,
             cluster_threshold,
             min_distance,
             height_control,
             alpha,
         )
+
         stat_map_svg = _stat_map_to_svg(
-            stat_img=thresholded_stat_map,
+            stat_img=thresholded_img,
+            threshold=threshold,
             bg_img=bg_img,
             cut_coords=cut_coords,
             display_mode=display_mode,
             plot_type=plot_type,
             table_details=table_details,
         )
+
         cluster_table = get_clusters_table(
-            stat_map_img,
+            thresholded_img,
             stat_threshold=threshold,
             cluster_threshold=cluster_threshold,
             min_distance=min_distance,
@@ -889,6 +899,7 @@ def _clustering_params_to_dataframe(
 @fill_doc
 def _stat_map_to_svg(
     stat_img,
+    threshold,
     bg_img,
     cut_coords,
     display_mode,
@@ -905,6 +916,9 @@ def _stat_map_to_svg(
        to be plotted as slices or glass brain.
        Does not perform any thresholding.
 
+    threshold : float
+       Desired threshold in z-scale.
+
     bg_img : Niimg-like object
         Only used when plot_type is 'slice'.
         See :ref:`extracting_data`.
@@ -945,13 +959,15 @@ def _stat_map_to_svg(
             bg_img=bg_img,
             cut_coords=cut_coords,
             display_mode=display_mode,
+            threshold=threshold,
         )
     elif plot_type == "glass":
         stat_map_plot = plot_glass_brain(
             stat_img,
             display_mode=display_mode,
             colorbar=True,
             plot_abs=False,
+            threshold=threshold,
         )
     else:
         raise ValueError(

nilearn/reporting/tests/test_glm_reporter.py

@@ -234,6 +234,7 @@ def test_stat_map_to_svg_slice_z(img_3d_mni, cut_coords):
         display_mode="ortho",
         plot_type="slice",
         table_details=table_details,
+        threshold=2.76,
     )
 
 
@@ -247,6 +248,7 @@ def test_stat_map_to_svg_glass_z(img_3d_mni, cut_coords):
         display_mode="z",
         plot_type="glass",
         table_details=table_details,
+        threshold=2.76,
     )
 
 
@@ -264,6 +266,7 @@ def test_stat_map_to_svg_invalid_plot_type(img_3d_mni, cut_coords):
             display_mode="z",
             plot_type="junk",
             table_details={"junk": 0},
+            threshold=2.76,
         )