{
  "analysis": "AMN--SCAN Kommula pairwise segregation from edge-wise Pearson r",
  "within_definition": "mean raw Pearson r across all within-network vertex pairs; self-connections excluded",
  "between_definition": "one undirected mean raw Pearson r across all AMN--SCAN vertex pairs",
  "segregation_definition": "SI_i_to_j=(W_i-B_AMN_SCAN)/(W_i+B_AMN_SCAN+2); arrows indicate reference network only",
  "segregation_reference": "Kommula Y, Callow DD, Purcell JJ, Smith JC. Acute Exercise Improves Large-Scale Brain Network Segregation in Healthy Older Adults. Brain Connect. 2024;14(7):369-381. doi:10.1089/brain.2024.0003.",
  "task_handling": "task state is the equal arithmetic mean of four run-specific metrics; run analyses retain runs 01--04 separately",
  "sample_policy": "A participant contributes only after restpre, all four task runs, and restpost succeed in both pipelines; subject_log.tsv records failures.",
  "models": {
    "separate_pipeline": "metric ~ state/run + meanFD + (1|subject)",
    "joint_sensitivity": "metric ~ pipeline * state/run + meanFD + (1|subject)"
  },
  "fdr": {
    "method": "Benjamini-Hochberg",
    "primary": "separately within analysis (state/run), pipeline, result type, and metric family; pairwise tests are further separated by contrast",
    "joint": "separately within analysis, fixed-effect term, and metric family",
    "joint_state_pipeline_interactions": "the three planned pipeline-by-state contrasts (task-restpre, restpost-restpre, restpost-task) are corrected together within the mechanism family and within the segregation family"
  },
  "atlas": "AMN nonzero fsaverage5; SCAN fs6 value 1.5 nearest-neighbour mapped to fsaverage5; overlapping vertices excluded from both",
  "atlas_qc": {
    "hemispheres": {
      "lh": {
        "amn_raw": 1112,
        "scan_raw": 159,
        "cortex": 9354,
        "overlap_removed": 3,
        "amn_final": 1109,
        "scan_final": 156
      },
      "rh": {
        "amn_raw": 1237,
        "scan_raw": 106,
        "cortex": 9361,
        "overlap_removed": 6,
        "amn_final": 1231,
        "scan_final": 100
      }
    },
    "total": {
      "amn_raw": 2349,
      "scan_raw": 265,
      "cortex": 18715,
      "overlap_removed": 9,
      "amn_final": 2340,
      "scan_final": 256
    }
  },
  "complete_case_coverage": {
    "primary": [
      {
        "analysis": "state",
        "pipeline": "withWM",
        "metric": "within_r_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "withWM",
        "metric": "within_r_SCAN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "withWM",
        "metric": "between_r_AMN_SCAN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "withWM",
        "metric": "segregation_r_AMN_to_SCAN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "withWM",
        "metric": "segregation_r_SCAN_to_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "regressWM",
        "metric": "within_r_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
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        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
        "pipeline": "regressWM",
        "metric": "between_r_AMN_SCAN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
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        "metric": "segregation_r_AMN_to_SCAN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "state",
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        "metric": "segregation_r_SCAN_to_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
        "excluded_levels": {}
      },
      {
        "analysis": "run",
        "pipeline": "withWM",
        "metric": "within_r_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
        "excluded_subject_ids": [],
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      },
      {
        "analysis": "run",
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      },
      {
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        "n_observed_subjects": 25,
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        "excluded_subject_ids": [],
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      },
      {
        "analysis": "run",
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      },
      {
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      },
      {
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      },
      {
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      },
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    ],
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        "metric": "within_r_AMN",
        "n_observed_subjects": 25,
        "n_complete_subjects": 25,
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        "excluded_levels": {}
      },
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        "n_complete_subjects": 25,
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        "excluded_levels": {}
      },
      {
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      },
      {
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      },
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    ]
  },
  "parameters": {
    "stats_root": "/DATA/wangxr_data/Flanker/analysis/03_stats",
    "wm_root": "/DATA/wangxr_data/Flanker/analysis/03_stats_new/Flanker_WM_regressed",
    "aroma_root": "/DATA/wangxr_data/Flanker/analysis/02_prepro/derivatives/aroma_6Asym",
    "prepro_root": "/DATA/wangxr_data/Flanker/analysis/02_prepro/derivatives/fmriprep_9cAsym",
    "confounds_root": "/DATA/wangxr_data/Flanker/analysis/02_prepro/derivatives/fmriprep_9cAsym",
    "subject_list": "/home/wangxr/Documents/data3/Flanker/scripts/sub.list",
    "subjects_dir": "/software/Tools/freesurfer/subjects",
    "amn_atlas_dir": "/home/wangxr/.cache/templateflow/tpl-Altas/AMN_Dosenbach",
    "scan_atlas_dir": "/home/wangxr/.cache/templateflow/tpl-Altas/SCAN_atlas_OSF_nmdka/Parcellation/Surface atlas",
    "nilearn_data_dir": null,
    "output_dir": "/DATA/wangxr_data/Flanker/analysis/04_QC/AMN_SCAN_partition/pairwise_segregation_mechanism",
    "block_size": 256,
    "overwrite": "1"
  }
}