functional connectivity, pylance, and other improvements

src/analysis/intergroupbrainimage.py

@@ -58,6 +58,13 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 }
 
 
+DESCRIPTION = """\n1. Group Contrast 2D/3D (plot_2d_3d_contrasts_between_groups)
+\nCompares two participant groups' contrast results (e.g. condition-vs-baseline effects) channel-by-channel, fitting a mixed-effects model with group, channel, and chromophore as factors. Produces BOTH directions of the contrast (Group A minus Group B, and Group B minus Group A) as separate plots, so the sign convention is explicit either way you read it.
+\nis_3d controls the display: True renders a 3D weighted brain map per contrast direction (same rendering as intra method 1, but showing the between-group difference rather than a single group's estimate); False renders a 2D topographic map instead, which is faster and sometimes easier to read at a glance for a whole-head pattern.
+\nA channel is only included if BOTH groups have at least min_participants_per_group (default 2) contributing participants for that channel - channels present in only one group, or with too few participants in either group to estimate within-group variance, are dropped before fitting. If this drops too many channels, check that both groups have enough participants with usable data for the selected event/channels.
+\nAs with other mixed-effects models in this app, small participant counts can produce convergence warnings; when that happens, the model falls back to pooled OLS, which does not account for the repeated-measures structure of the data and may understate uncertainty - treat results run this way with extra caution.
+"""
+
 
 class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
     def __init__(
@@ -77,7 +84,7 @@ class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
         self.contrast_results_dict = contrast_results_dict
         self.group_dict = group_dict
 
-        self.setup_inter_group_ui(["0 (Contrast Image)"])
+        self.setup_inter_group_ui(["0 (Group Contrast 2D/3D)"], placeholder_text=DESCRIPTION)
 
 
     def process_request(self):