{
    "tree_id": "demo_external_regressors_single_model",
    "info": "Demonstration based on the minimal decision tree that uses an F stat on a model with multiple external regressors.",
    "report": "This is based on the minimal criteria of the original MEICA decision tree \\citep{kundu2013integrated} without the more aggressive noise removal steps \\citep{dupre2021te}.",
    "necessary_metrics": [
        "kappa",
        "rho",
        "countsigFS0",
        "countsigFT2",
        "dice_FS0",
        "dice_FT2",
        "signal-noise_t",
        "variance explained",
        "pval nuisance model",
        "R2stat nuisance model"
    ],
    "intermediate_classifications": ["provisionalaccept", "provisionalreject"],
    "classification_tags": ["Likely BOLD", "Unlikely BOLD", "Low variance", "External regressors"],
    "external_regressor_config": [
        {
            "regress_ID": "nuisance",
            "info": "Fits all external nuisance regressors to a single model using an F statistic",
            "report": "External nuisance regressors that fit to components using a linear model were rejected.",
            "detrend": true,
            "statistic": "F",
            "regressors": ["trans_x","trans_y","trans_z","rot_x","rot_y","rot_z","csf","white_matter"]
        }
    ],
    "nodes": [
        {
            "functionname": "manual_classify",
            "parameters": {"new_classification": "unclassified", "decide_comps": "all"},
            "kwargs": {"clear_classification_tags": true, "dont_warn_reclassify": true}
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "rejected",
                "if_false": "nochange",
                "decide_comps": "all",
                "op": ">",
                "left": "rho",
                "right": "kappa"
            },
            "kwargs": {"tag_if_true": "Unlikely BOLD"}
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "rejected",
                "if_false": "nochange",
                "decide_comps": "all",
                "op": ">",
                "left": "countsigFS0",
                "right": "countsigFT2"
            },
            "kwargs": {
                "left2": "countsigFT2",
                "op2": ">",
                "right2": 0,
                "tag_if_true": "Unlikely BOLD"
            }
        },
        {
            "functionname": "calc_median",
            "parameters": {
                "decide_comps": "all",
                "metric_name": "variance explained",
                "median_label": "varex"
            }
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "rejected",
                "if_false": "nochange",
                "decide_comps": "all",
                "op": ">",
                "left": "dice_FS0",
                "right": "dice_FT2"
            },
            "kwargs": {
                "left2": "variance explained",
                "op2": ">",
                "right2": "median_varex",
                "tag_if_true": "Unlikely BOLD"
            }
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "rejected",
                "if_false": "nochange",
                "decide_comps": "all",
                "op": ">",
                "left": 0,
                "right": "signal-noise_t"
            },
            "kwargs": {
                "left2": "variance explained",
                "op2": ">",
                "right2": "median_varex",
                "tag_if_true": "Unlikely BOLD"
            }
        },
        {
            "functionname": "calc_kappa_elbow",
            "parameters": {"decide_comps": "all"},
            "_comment": ""
        },
        {
            "functionname": "calc_rho_elbow",
            "parameters": {"decide_comps": "all"},
            "kwargs": {"subset_decide_comps": "unclassified", "rho_elbow_type": "liberal"},
            "_comment": ""
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "provisionalaccept",
                "if_false": "provisionalreject",
                "decide_comps": "unclassified",
                "op": ">=",
                "left": "kappa",
                "right": "kappa_elbow_kundu"
            }
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "provisionalreject",
                "if_false": "nochange",
                "decide_comps": ["provisionalreject", "provisionalaccept"],
                "op": ">",
                "left": "rho",
                "right": "rho_elbow_liberal"
            }
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "provisionalaccept",
                "if_false": "nochange",
                "decide_comps": "provisionalreject",
                "op": ">",
                "left": "kappa",
                "right": "rho"
            },
            "kwargs": {
                "log_extra_info": "If kappa>elbow and kappa>2*rho accept even if rho>elbow",
                "right_scale": 2,
                "op2": ">",
                "left2": "kappa",
                "right2": "kappa_elbow_kundu",
                "tag_if_true": "Likely BOLD"
            }
        },
        {
            "functionname": "dec_left_op_right",
            "parameters": {
                "if_true": "rejected",
                "if_false": "nochange",
                "decide_comps": "all",
                "op": "<",
                "left": "pval nuisance model",
                "right": 0.05
            },
            "kwargs": {
                "op2": ">",
                "left2": "R2stat nuisance model",
                "right2": 0.5,
                "log_extra_info": "If external regressors fit with p<0.05 and model R2>0.5 of the variance, then reject.",
                "tag_if_true": "External regressors"
            }
        },
        {
            "functionname": "dec_variance_lessthan_thresholds",
            "parameters": {
                "if_true": "accepted",
                "if_false": "nochange",
                "decide_comps": "provisionalreject"
            },
            "kwargs": {
                "var_metric": "variance explained",
                "single_comp_threshold": 0.1,
                "all_comp_threshold": 1.0,
                "tag_if_true": "Low variance"
            }
        },

        {
            "functionname": "manual_classify",
            "parameters": {"new_classification": "accepted", "decide_comps": "provisionalaccept"},
            "kwargs": {"tag": "Likely BOLD"}
        },
        {
            "functionname": "manual_classify",
            "parameters": {
                "new_classification": "rejected",
                "decide_comps": ["provisionalreject", "unclassified"]
            },
            "kwargs": {"tag": "Unlikely BOLD"}
        }
    ]
}