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Add elbow-less minimal decision tree #1131

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Add elbow-less minimal decision tree #1131

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148 changes: 148 additions & 0 deletions tedana/resources/decision_trees/elbowless_minimal.json
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{
"tree_id": "elbowless_minimal_decision_tree",
"info": "first version of minimal decision tree without elbows",
"report": "The elbow-less minimal decision tree \\citep{tedana_decision_trees} is a simplified version of the MEICA decision tree \\citep{kundu2013integrated,dupre2021te} without many criteria that do not rely on kappa and rho thresholds, including any criteria based on elbows calculated across components. ",
"necessary_metrics": [
"kappa",
"rho",
"countsigFS0",
"countsigFT2",
"dice_FS0",
"dice_FT2",
"signal-noise_t",
"variance explained"
],
"intermediate_classifications": ["provisionalaccept", "provisionalreject"],
"classification_tags": ["Likely BOLD", "Unlikely BOLD", "Low variance"],
"_comment": "More information on the minimial decision tree and how it differs from other options is at https://tedana.readthedocs.io/en/stable/included_decision_trees.html. Descriptions of the metrics used are in desc-tedana_metrics.json, which is ouputted when this tree is run",
"nodes": [
{
"functionname": "manual_classify",
"parameters": {"new_classification": "unclassified", "decide_comps": "all"},
"kwargs": {
"clear_classification_tags": true,
"dont_warn_reclassify": true
},
"_comment": "All components are initially labeled as 'unclassified'."
},
{
"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"},
"_comment": "The first four steps are for rejecting components that very unlikely to have substantial T2* signal. Any components with rho greater than kappa are rejected. Higher rho than kappa means that the component better fits the TE-independence (S0) model than the TE-dependence (T2*) model."
},
{
"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"
},
"_comment": "Any components with more voxels that are significant based on the S0 model's F-statistics than the T2* model's are rejected, as long as there is at least one significant voxel for the T2 model."
},
{
"functionname": "calc_median",
"parameters": {
"decide_comps": "all",
"metric_name": "variance explained",
"median_label": "varex"
},
"_comment": "The median variance explained is calculated across all components, for use in later steps."
},
{
"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"
},
"_comment": "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. In slightly plainer English, this step rejects any high-variance components where significant voxels in the F-stat map overlap more with highly S0-associated voxels than T2*-associated voxels."
},
{
"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"
},
"_comment": "Any components with a negative t-statistic comparing the 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. That is reject any high-variance components exhibiting more 'speckled' T2*-associated voxels than 'clustered' ones."
},
{
"functionname": "dec_left_op_right",
"parameters": {
"if_true": "accepted",
"if_false": "nochange",
"decide_comps": "provisionalaccept",
"op": ">",
"left": "kappa",
"right": "rho"
},
"kwargs": {"right_scale": 2, "tag_if_true": "Likely BOLD"},
"_comment": "Any provisionally accepted components with kappa greater than two times rho are accepted. That is, even if a component has a high rho value, if kappa above threshold and substantially higher, assume it as something work keeping and accept it"
},
{
"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"
},
"_comment": "This step flags remaining low-variance components (less than 0.1%) and accepts up to 1% cumulative variance across these components. This is done because these components don't explain enough variance to be worth further reducing the degrees of freedom of the denoised data."
},
{
"functionname": "manual_classify",
"parameters": {"new_classification": "accepted", "decide_comps": "provisionalaccept"},
"kwargs": {"tag": "Likely BOLD"},
"_comment": "All remaining provisionally accepted components are accepted."
},
{
"functionname": "manual_classify",
"parameters": {
"new_classification": "rejected",
"decide_comps": ["provisionalreject", "unclassified"]
},
"kwargs": {"tag": "Unlikely BOLD"},
"_comment": "All remaining unclassified (nothing should be unclassified) or provisionally rejected components are rejected."
}
]
}