Document decision tree steps in report

tedana/resources/decision_trees/minimal.json

@@ -30,10 +30,12 @@
                 "decide_comps": "all"
             },
             "kwargs": {
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "All components are initially labeled as 'unclassified'.",
                 "clear_classification_tags": true,
                 "dont_warn_reclassify": true
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_left_op_right",
@@ -46,9 +48,11 @@
                 "right": "kappa"
             },
             "kwargs": {
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "Any components with rho greater than kappa are rejected.",
                 "tag_if_true": "Unlikely BOLD"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_left_op_right",
@@ -64,17 +68,24 @@
                 "left2": "countsigFT2",
                 "op2": ">",
                 "right2": 0,
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "Any components with higher S0 model beta map-F-statistic map Dice similarity index than T2 model beta map-F-statistic map Dice similarity index and greater than median variance explained are rejected.",
                 "tag_if_true": "Unlikely BOLD"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "calc_median",
             "parameters": {
                 "decide_comps": "all",
                 "metric_name": "variance explained",
                 "median_label": "varex"
-            }
+            },
+            "kwargs": {
+                "log_extra_info": "",
+                "log_extra_report": "The median variance explained is calculated across all components, for later steps."
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_left_op_right",
@@ -90,9 +101,11 @@
                 "left2": "variance explained",
                 "op2": ">",
                 "right2": "median_varex",
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "Any components with higher S0 model beta map-F-statistic map Dice similarity index than T2 model beta map-F-statistic map Dice similarity index and greater than median variance explained are rejected.",
                 "tag_if_true": "Unlikely BOLD"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_left_op_right",
@@ -108,9 +121,11 @@
                 "left2": "variance explained",
                 "op2": ">",
                 "right2": "median_varex",
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "Any components with negative t-statistic comparing distribution of T2* model F-statistics from voxels in clusters to those of voxels not in clusters and variance explained greater than median are rejected.",
                 "tag_if_true": "Unlikely BOLD"
-            }
+            },
+            "_comment": "This essentially rejects any components with high variance explained and exhibiting more 'speckled' T2*-associated voxels than 'clustered' ones."
         },
         {
             "functionname": "calc_kappa_elbow",
@@ -119,7 +134,7 @@
             },
             "kwargs": {
                 "log_extra_info": "",
-                "log_extra_report": ""
+                "log_extra_report": "The kappa elbow is calculated from all components, for later steps."
             },
             "_comment": ""
         },
@@ -132,7 +147,7 @@
                 "subset_decide_comps": "unclassified",
                 "rho_elbow_type": "liberal",
                 "log_extra_info": "",
-                "log_extra_report": ""
+                "log_extra_report": "The 'liberal' rho elbow is calculated from all (unclassified?) components, for later steps."
             },
             "_comment": ""
         },
@@ -147,8 +162,10 @@
                 "right": "kappa_elbow_kundu"
             },
             "kwargs": {
-                "log_extra_report": ""
-            }
+                "log_extra_info": "",
+                "log_extra_report": "Any unclassified components with kappa greater than or equal to the kappa elbow are provisionally accepted. Any remaining unclassified components are provisionally rejected."
+            },
+            "_comment": "This step provisionally classifies all 'unclassified' components."
         },
         {
             "functionname": "dec_left_op_right",
@@ -161,11 +178,12 @@
                 "right": "rho"
             },
             "kwargs": {
-                "log_extra_info": "If kappa>elbow and kappa>2*rho accept even if rho>elbow",
-                "log_extra_report": "",
+                "log_extra_info": "",
+                "log_extra_report": "Any provisionally accepted components with kappa greater than two times rho are accepted.",
                 "right_scale": 2,
                 "tag_if_true": "Likely BOLD"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_left_op_right",
@@ -181,8 +199,10 @@
                 "right": "rho_elbow_liberal"
             },
             "kwargs": {
-                "log_extra_report": ""
-            }
+                "log_extra_info": "",
+                "log_extra_report": "Any provisionally accepted and provisionally rejected components with rho values greater than the liberal rho elbow are provisionally rejected."
+            },
+            "_comment": ""
         },
         {
             "functionname": "dec_variance_lessthan_thresholds",
@@ -194,11 +214,12 @@
             "kwargs": {
                 "var_metric": "variance explained",
                 "log_extra_info": "",
-                "log_extra_report": "",
+                "log_extra_report": "Any provisionally rejected components with variance explained less than ? are accepted.",
                 "single_comp_threshold": 0.1,
                 "all_comp_threshold": 1.0,
                 "tag_if_true": "Low variance"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "manual_classify",
@@ -208,9 +229,10 @@
             },
             "kwargs": {
                 "log_extra_info": "",
-                "log_extra_report": "",
+                "log_extra_report": "All remaining provisionally accepted components are accepted.",
                 "tag": "Likely BOLD"
-            }
+            },
+            "_comment": ""
         },
         {
             "functionname": "manual_classify",
@@ -223,9 +245,10 @@
             },
             "kwargs": {
                 "log_extra_info": "",
-                "log_extra_report": "",
+                "log_extra_report": "All remaining unclassified or provisionally rejected components are rejected.",
                 "tag": "Unlikely BOLD"
-            }
+            },
+            "_comment": "Are unclassified components even possible at this point?"
         }
     ]
 }