Overview

This report runs the merged resting-state FC analysis that keeps the covariate-adjusted regression model from the Aim 1 script and applies the hypothesis-selected ROI pairs from the enhanced analysis framework.

The input files are read from:

The analysis writes results to:

Run Analysis

source("3 resting_state_fc_mdd_hypothesis_targeted.R", local = TRUE)
## 
## Merged FC analysis complete. Outputs saved to:
## C:\Users\quent\Desktop\fmri eye\data\aim1_hypothesis_outputs
## Model used: fc_value ~ Group + age + Sex + ICV 
## Motion status: not_found 
##         analysis           subset                            formula rows_used
##           <char>           <char>                             <char>     <int>
## 1: full_edgewise        all_edges fc_value ~ Group + age + Sex + ICV   3606498
## 2: theory_driven           H1_DMN fc_value ~ Group + age + Sex + ICV       609
## 3: theory_driven      H2_Salience fc_value ~ Group + age + Sex + ICV      1218
## 4: theory_driven        H3_Reward fc_value ~ Group + age + Sex + ICV       812
## 5: theory_driven     H4_Brainstem fc_value ~ Group + age + Sex + ICV      1015
## 6: theory_driven H5_Interoceptive fc_value ~ Group + age + Sex + ICV      1218
##    n_edges_tested n_sig_uncorrected_p_lt_0_05 n_sig_fdr_bh_q_lt_0_05
##             <int>                       <int>                  <int>
## 1:          17766                         870                      0
## 2:              3                           3                      3
## 3:              6                           5                      5
## 4:              4                           2                      2
## 5:              5                           5                      5
## 6:              6                           3                      3
##    n_sig_bonf_p_lt_0_05 min_p_uncorrected
##                   <int>             <num>
## 1:                    0      6.137918e-05
## 2:                    3      6.137918e-05
## 3:                    2      1.565933e-04
## 4:                    2      1.497745e-04
## 5:                    4      3.240282e-04
## 6:                    3      3.842197e-04

Analysis Summary

summary_path <- file.path(out_dir, "analysis_summary_counts.csv")
summary_dt <- fread(summary_path)
kable(summary_dt)
analysis subset formula rows_used n_edges_tested n_sig_uncorrected_p_lt_0_05 n_sig_fdr_bh_q_lt_0_05 n_sig_bonf_p_lt_0_05 min_p_uncorrected
full_edgewise all_edges fc_value ~ Group + age + Sex + ICV 3606498 17766 870 0 0 0.0000614
theory_driven H1_DMN fc_value ~ Group + age + Sex + ICV 609 3 3 3 3 0.0000614
theory_driven H2_Salience fc_value ~ Group + age + Sex + ICV 1218 6 5 5 2 0.0001566
theory_driven H3_Reward fc_value ~ Group + age + Sex + ICV 812 4 2 2 2 0.0001498
theory_driven H4_Brainstem fc_value ~ Group + age + Sex + ICV 1015 5 5 5 4 0.0003240
theory_driven H5_Interoceptive fc_value ~ Group + age + Sex + ICV 1218 6 3 3 3 0.0003842 
meta_path <- file.path(out_dir, "run_metadata.csv")
meta_dt <- fread(meta_path)
kable(meta_dt)
meta_key value
data_dir C:eye
fc_file C:eye/FC_data_aligned_long.csv
icv_align_file C:eye/ICV_measures_aligned.csv
demog_file C:eye/Data1.csv
dedup_strategy prefer_unsuffixed
model_formula fc_value ~ Group + age + Sex + ICV
motion_detection_status not_found
n_subject_rows 205
n_edge_rows 3606498

Hypothesis Definitions

hypothesis_path <- file.path(out_dir, "hypothesis_edge_definitions.csv")
hypothesis_dt <- fread(hypothesis_path)
kable(hypothesis_dt)
hypothesis node1 node2 FC
H1_DMN 51 181 FC51_181
H1_DMN 125 181 FC125_181
H1_DMN 98 161 FC98_161
H2_Salience 48 155 FC48_155
H2_Salience 122 155 FC122_155
H2_Salience 48 156 FC48_156
H2_Salience 122 156 FC122_156
H2_Salience 48 80 FC48_80
H2_Salience 80 122 FC80_122
H3_Reward 16 43 FC16_43
H3_Reward 16 117 FC16_117
H3_Reward 16 60 FC16_60
H3_Reward 16 134 FC16_134
H4_Brainstem 12 160 FC12_160
H4_Brainstem 12 143 FC12_143
H4_Brainstem 12 69 FC12_69
H4_Brainstem 12 118 FC12_118
H4_Brainstem 12 44 FC12_44
H5_Interoceptive 80 89 FC80_89
H5_Interoceptive 80 90 FC80_90
H5_Interoceptive 89 90 FC89_90
H5_Interoceptive 60 90 FC60_90
H5_Interoceptive 155 163 FC155_163
H5_Interoceptive 155 164 FC155_164

Full Edgewise Results

full_path <- file.path(out_dir, "full_model_all_edges.csv")
full_dt <- fread(full_path)
kable(head(full_dt, 20))
FC beta_group se t p_uncorrected n p_fdr_bh p_fwer_bonf node1 node2
FC51_181 -0.1239294 0.0302604 -4.095439 0.0000614 203 0.8095509 1 51 181
FC16_43 0.0800840 0.0207131 3.866338 0.0001498 203 0.8095509 1 16 43
FC48_155 -0.1308619 0.0339492 -3.854636 0.0001566 203 0.8095509 1 48 155
FC109_118 0.1054081 0.0284355 3.706916 0.0002723 203 0.8095509 1 109 118
FC12_160 0.1100701 0.0300778 3.659520 0.0003240 203 0.8095509 1 12 160
FC60_90 -0.1162063 0.0321665 -3.612651 0.0003842 203 0.8095509 1 60 90
FC80_89 -0.0914126 0.0256647 -3.561795 0.0004614 203 0.8095509 1 80 89
FC122_155 -0.1306761 0.0370613 -3.525946 0.0005243 203 0.8095509 1 122 155
FC125_181 -0.0948620 0.0271008 -3.500336 0.0005740 203 0.8095509 1 125 181
FC98_161 -0.1168334 0.0335601 -3.481319 0.0006138 203 0.8095509 1 98 161
FC48_69 0.1226250 0.0352555 3.478186 0.0006206 203 0.8095509 1 48 69
FC17_100 -0.0831210 0.0241728 -3.438613 0.0007128 203 0.8095509 1 17 100
FC155_168 -0.1102251 0.0321003 -3.433772 0.0007249 203 0.8095509 1 155 168
FC9_103 -0.0770023 0.0227366 -3.386715 0.0008531 203 0.8095509 1 9 103
FC62_96 0.0879938 0.0260564 3.377051 0.0008820 203 0.8095509 1 62 96
FC28_96 -0.0837193 0.0249458 -3.356055 0.0009478 203 0.8095509 1 28 96
FC60_164 -0.1131580 0.0337544 -3.352390 0.0009597 203 0.8095509 1 60 164
FC74_80 -0.0883514 0.0263794 -3.349263 0.0009700 203 0.8095509 1 74 80
FC28_95 -0.0886636 0.0265465 -3.339938 0.0010014 203 0.8095509 1 28 95
FC12_143 0.0990458 0.0297542 3.328798 0.0010401 203 0.8095509 1 12 143

Theory-Driven Results

theory_path <- file.path(out_dir, "theory_driven_results_all.csv")
if (file.exists(theory_path)) {
  theory_dt <- fread(theory_path)
  kable(head(theory_dt, 20))
} else {
  cat("No theory-driven results were written for this run.\n")
}
hypothesis FC beta_group se t p_uncorrected n p_fdr_bh p_fwer_bonf node1 node2 n_edges_defined
H1_DMN FC51_181 -0.1239294 0.0302604 -4.0954387 0.0000614 203 0.0001841 0.0001841 51 181 3
H1_DMN FC125_181 -0.0948620 0.0271008 -3.5003360 0.0005740 203 0.0006138 0.0017221 125 181 3
H1_DMN FC98_161 -0.1168334 0.0335601 -3.4813187 0.0006138 203 0.0006138 0.0018414 98 161 3
H2_Salience FC48_155 -0.1308619 0.0339492 -3.8546365 0.0001566 203 0.0009396 0.0009396 48 155 6
H2_Salience FC122_155 -0.1306761 0.0370613 -3.5259461 0.0005243 203 0.0015728 0.0031456 122 155 6
H2_Salience FC122_156 0.0827737 0.0336598 2.4591277 0.0147858 203 0.0295716 0.0887148 122 156 6
H2_Salience FC48_80 -0.0780029 0.0337018 -2.3145009 0.0216658 203 0.0324987 0.1299946 48 80 6
H2_Salience FC48_156 0.0740557 0.0333235 2.2223235 0.0273932 203 0.0328718 0.1643592 48 156 6
H2_Salience FC80_122 -0.0458962 0.0340350 -1.3484992 0.1790383 203 0.1790383 1.0000000 80 122 6
H3_Reward FC16_43 0.0800840 0.0207131 3.8663383 0.0001498 203 0.0005991 0.0005991 16 43 4
H3_Reward FC16_117 0.0681396 0.0209297 3.2556385 0.0013308 203 0.0026616 0.0053232 16 117 4
H3_Reward FC16_134 -0.0227444 0.0249430 -0.9118531 0.3629549 203 0.4839399 1.0000000 16 134 4
H3_Reward FC16_60 -0.0046459 0.0261034 -0.1779802 0.8589205 203 0.8589205 1.0000000 16 60 4
H4_Brainstem FC12_160 0.1100701 0.0300778 3.6595200 0.0003240 203 0.0016201 0.0016201 12 160 5
H4_Brainstem FC12_143 0.0990458 0.0297542 3.3287982 0.0010401 203 0.0020867 0.0052003 12 143 5
H4_Brainstem FC12_69 0.0912093 0.0278598 3.2738719 0.0012520 203 0.0020867 0.0062600 12 69 5
H4_Brainstem FC12_118 0.0782873 0.0287744 2.7207308 0.0070937 203 0.0088671 0.0354685 12 118 5
H4_Brainstem FC12_44 0.0639127 0.0284333 2.2478135 0.0256907 203 0.0256907 0.1284535 12 44 5
H5_Interoceptive FC60_90 -0.1162063 0.0321665 -3.6126508 0.0003842 203 0.0013841 0.0023053 60 90 6
H5_Interoceptive FC80_89 -0.0914126 0.0256647 -3.5617953 0.0004614 203 0.0013841 0.0027682 80 89 6