Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control.
The 18 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
- [1] § Results › Between-subjects and within-subjects analysis of brain-behavior associations ↔ taskfmri/6_plotting/plotting_utils.py, lines 9–24 · score 0.90 · basal ganglia, AntSalience, PostSalience, VisualAssoc, lFPN, rFPN
- [2] § Methods › Inclusion criteria ↔ taskfmri/0_subjectlist/inclusions_1.py, lines 70–126 · score 0.88 · abcd_imgincl01.txt, iqc_sst_good_ser, mriqcrp20301.txt, imgincl sst
- [3] § Results › Between-subjects and within-subjects analysis of brain-behavior associations ↔ taskfmri/6_plotting/plotting_utils.py, lines 4–7 · score 0.86 · AntSalience, BasalGanglia, PostSalience, VisualAssoc, lFPN, rFPN
- [4] § Results › Within-subjects analysis reveals that subgroups with distinct control strategies have distinct brain-behavior associations ↔ taskfmri/6_plotting/plotting_utils.py, lines 4–7 · score 0.85 · AntSalience, BasalGanglia, PostSalience, VisualAssoc, lFPN, rFPN
- [5] § Methods › Networks and regions of interest ↔ image_masks/make_DMN.py, the whole file · a weak match · score 0.82 · connected_components, connected_regions, Neurosynth automatic, retrieved, masks
- [6] § Methods › Between- and within-subjects, general linear model analysis of fMRI ↔ taskfmri/6_plotting/ds_WB.py, lines 71–119 · score 0.81 · fetch_surf_fsaverage, plot_surf_stat_map, nilearn, mesh, surface, brain
- [7] § Methods › Networks and regions of interest ↔ image_masks/make_subcortical_ROIs.py, lines 1–10 · score 0.80 · nonlinear asymmetric space, high resolution, MNI152, masks, subcortical, thresholded
- [8] § Methods › Inclusion criteria ↔ taskfmri/0_subjectlist/inclusions_1_scanner_info_included_family_member.py, lines 25–78 · score 0.72 · genetic paired subjectid, pihat, siblings, family, scanner, variables
- [9] § Methods › Networks and regions of interest ↔ taskfmri/6_plotting/resample.ipynb, lines 4–49 · score 0.69 · subcortical regions, Shirer regions, cognitive control regions, Shirer networks, Yeo, Pearson
- [10] § Methods › Brain imaging ↔ taskfmri/1_preprocess/im_proc.py, lines 31–88 · score 0.68 · smooth_img, affine, template, epi, motion, volumes
- [11] § Methods › Networks and regions of interest ↔ taskfmri/5_more_second_level/resample.py, lines 87–134 · score 0.66 · subcortical regions, Shirer regions, cognitive control regions, Shirer networks, Yeo, Pearson
- [12] § Methods › Between- and within-subjects, general linear model analysis of fMRI ↔ taskfmri/3_individualstats/individualstats.py, lines 126–175 · score 0.64 · FirstLevelModel, design matrices, nilearn, signal, fit, models
- [13] § Methods › Statistical testing ↔ taskfmri/5_more_second_level/permutations.ipynb, lines 390–475 · score 0.63 · permutation_test, Pearson correlation, correct go, coefficients, resamples, SSRT
- [14] § Results › Nonergodic brain-behavior associations using observed reaction time ↔ taskfmri/4_groupstats/groupstats.py, lines 165–295 · score 0.61 · dorsal attention, salience network, sensorimotor, precuneus, anterior, posterior
- [15] § Methods › Statistical testing ↔ taskfmri/5_more_second_level/permutations.ipynb, lines 60–106 · score 0.57 · false_discovery_control, permutation_test, Scipy
- [16] § Methods › Representational similarity analysis ↔ taskfmri/6_plotting/rsa.ipynb, lines 58–89 · score 0.56 · common_norm, kdeplot, Density, clip, proactive delaying, correlation
- [17] § Methods › Between- and within-subjects, general linear model analysis of fMRI ↔ taskfmri/3_individualstats/individualstats.py, lines 57–68 · score 0.55 · FirstLevelModel, regression coefficients, voxel, fit, SST, fMRI
- [18] § Results › Dynamic cognitive process model of behavior ↔ taskfmri/6_plotting/overview.ipynb, lines 219–260 · score 0.53 · stopping expectancy, Stop signal, go process, arrow, proactivity
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
The paper is loaded when this pane is shown.
The authors' code
Python · 27 lines · 870 B · no license · 3 matches
- """Utilities used for plotting."""
- # Order of Shirer networks:
- SHIRER_ORDER = ['AntSalience','PostSalience','lFPN','rFPN','DMN','RSC/PHG',
- 'Precuneus','Visuospatial','Language','VisualAssoc','Visual','Auditory',
- 'Sensorimotor','BasalGanglia']
- # Mapping from network names used in code to network names used in plots:
- MAPPING = {
- # Yeo-17
- 'SalVentAttn-1':'SalVAttn-1',
- 'SalVentAttn-2':'SalVAttn-2',
- # Shirer networks
- 'anterior_Salience':'AntSalience',
- 'post_Salience':'PostSalience',
- 'LECN':'lFPN',
- 'RECN':'rFPN',
- 'dorsal_DMN':'DMN',
- 'ventral_DMN':'RSC/PHG',
- 'high_Visual':'VisualAssoc',
- 'prim_Visual':'Visual',
- 'Basal_Ganglia':'BasalGanglia',
- }
- def final_roi_names(roi_names):
- return [MAPPING[roi] if roi in MAPPING else roi for roi in roi_names]
plotting_utils.py at commit b066a52, no license · at the source
Overview
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, CA USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA USA
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA USA
Abstract
Nonergodicity and Simpson’s paradox present significant, yet underappreciated challenges in cognitive neuroscience. Leveraging brain imaging and behavioral data from over 4000 individuals and a Bayesian computational model of cognitive dynamics, we investigated brain-behavior relationships underlying cognitive control at both between-subjects and within-subjects levels. Strikingly, brain-behavior associations reversed across levels of analysis, revealing pervasive nonergodicity. Within-subjects analysis uncovered dissociated neural representations of reactive and proactive control and revealed that individuals who adaptively versus maladaptively regulated cognitive control exhibited distinct brain-behavior associations. Our findings demonstrate that between-subjects analyses can fundamentally mischaracterize within-individuals mechanisms, as group-level patterns not only disagreed with individual-level patterns but often reversed them. This work highlights the necessity of distinguishing between-subjects and within-subjects inferences in neuroscience, with implications for understanding cognitive mechanisms and designing personalized interventions.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 18 matches between paragraphs and lines of code.
Zenodo 18626601
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
- 30 September 2026: the link answers (HTTP 200)
75 files
- PRAD_Behavioral_Dynamics
/ , MATLAB, 40 linesStartHere_PRADs.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 451 linesSummarizeResults.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 144 lineschkconv.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 904 linesmatjagsRAND.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 109 linessst_jags_and_save.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 203 linessst_prepare_for_jags.m - behavioral/
correlations.py , Python, 166 lines - behavioral/
get_SST_pm_behav.m , MATLAB, 14 lines - behavioral/
get_SST_pm_cog.m , MATLAB, 6 lines - behavioral/
get_SST_pm_cog_control_m , Python, 57 linesodels.py - behavioral/
get_SST_pm_cog_control_m , Python, 34 linesodels_test.py - behavioral/
npz_rip_cog_behav.py , Python, 72 lines - behavioral/
npz_rip_cog_behav_test.p , Python, 29 linesy - get_prad.sh, Shell, 7 lines
- image_masks/
make_DMN.py , Python, 29 lines - image_masks/
make_dACC.py , Python, 23 lines - image_masks/
make_subcortical_ROIs.py , Python, 40 lines - paths.py, Python, 31 lines
- taskfmri/
0_subjectlist/ , Python, 483 linesinclusions_1.py - taskfmri/
0_subjectlist/ , Python, 90 linesinclusions_1_scanner_inf o_included_family_member .py - taskfmri/
0_subjectlist/ , Python, 35 linesinclusions_control_model s.py - taskfmri/
0_subjectlist/ , Python, 36 linessex.py - taskfmri/
0_subjectlist/ , Python, 112 linessl.py - taskfmri/
0_subjectlist/ , Python, 24 linessl_test.py - taskfmri/
1_preprocess/ , Python, 100 linesim_proc.py - taskfmri/
1_preprocess/ , Shell, 16 linesim_proc.sh - taskfmri/
2_design/ , Python, 659 linesdesign.py - taskfmri/
2_design/ , Python, 83 linesrun_design.py - taskfmri/
2_design/ , Python, 69 linesrun_design_pradG.py - taskfmri/
2_design/ , Python, 69 linesrun_design_pradIR.py - taskfmri/
2_design/ , Python, 67 linesrun_design_rvm.py - taskfmri/
3_individualstats/ , Python, 182 linesindividualstats.py - taskfmri/
3_individualstats/ , Python, 82 linesrun_individualstats.py - taskfmri/
3_individualstats/ , Python, 88 linesrun_individualstats_oom. py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_prad G.py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_prad IR.py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_rvm. py - taskfmri/
4_groupstats/ , Python, 617 linesgroupstats.py - taskfmri/
4_groupstats/ , Python, 132 linesgroupstats_one_sample_WB .py - taskfmri/
4_groupstats/ , Python, 75 linesgroupstats_rema.py - taskfmri/
4_groupstats/ , Python, 27 linesprint_n.py - taskfmri/
4_groupstats/ , Python, 58 linesrun_groupstats_one_sampl e_WB.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_pradG.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_pradIR.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_rvm.py - taskfmri/
4_groupstats/ , Jupyter, 50 linessubject_average_mods.ipy nb - taskfmri/
5_more_second_level/ , Jupyter, 108 linesanatomical_nonergodicity .ipynb - taskfmri/
5_more_second_level/ , Jupyter, 475 linespermutations.ipynb - taskfmri/
5_more_second_level/ , Python, 27 linespermutations.py - taskfmri/
5_more_second_level/ , Python, 151 linesresample.py - taskfmri/
5_more_second_level/ , Python, 98 linesrsa.py - taskfmri/
6_plotting/ , Jupyter, 224 linesanatomical_nonergodicity .ipynb - taskfmri/
6_plotting/ , Jupyter, 336 linescompare_correlations_ds. ipynb - taskfmri/
6_plotting/ , Python, 22 linescompare_correlations_ds_ test.py - taskfmri/
6_plotting/ , Python, 120 linescorrelate_betas_WB.py - taskfmri/
6_plotting/ , Python, 151 linesds_WB.py - taskfmri/
6_plotting/ , Python, 91 linesds_WB_control_models.py - taskfmri/
6_plotting/ , Jupyter, 324 linesoverview.ipynb - taskfmri/
6_plotting/ , Python, 27 linesplotting_utils.py - taskfmri/
6_plotting/ , Python, 100 linesprint_p_values.py - taskfmri/
6_plotting/ , Python, 112 linesreliability_group.py - taskfmri/
6_plotting/ , Python, 175 linesreliability_individual.p y - taskfmri/
6_plotting/ , Python, 149 linesrema.py - taskfmri/
6_plotting/ , Jupyter, 110 linesresample.ipynb - taskfmri/
6_plotting/ , Jupyter, 257 linesrsa.ipynb - taskfmri/
6_plotting/ , Jupyter, 240 linessubgroups.ipynb - taskfmri/
6_plotting/ , Python, 132 lineswithin_subjects_distribu tions.py - taskfmri/
make_source_data.sh , Shell, 59 lines - taskfmri/
submit_chain.sh , Shell, 21 lines - utilities/
backup_data_to_box.py , Python, 19 lines - utilities/
backup_results_to_box.py , Python, 30 lines - utilities/
parallel.py , Python, 19 lines - utilities/
report_error.py , Python, 32 lines - utilities/
submit.py , Python, 221 lines - README.md, Text, 118 lines
scsnl/mistry_branigan_nonergodicity_2026
b066a52ce857aff8287f75ae6971f15c3b4815a1, 12 February 2026Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
75 files
- PRAD_Behavioral_Dynamics
/ , MATLAB, 40 linesStartHere_PRADs.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 451 linesSummarizeResults.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 144 lineschkconv.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 904 linesmatjagsRAND.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 109 linessst_jags_and_save.m - PRAD_Behavioral_Dynamics
/ , MATLAB, 203 linessst_prepare_for_jags.m - behavioral/
correlations.py , Python, 166 lines - behavioral/
get_SST_pm_behav.m , MATLAB, 14 lines - behavioral/
get_SST_pm_cog.m , MATLAB, 6 lines - behavioral/
get_SST_pm_cog_control_m , Python, 57 linesodels.py - behavioral/
get_SST_pm_cog_control_m , Python, 34 linesodels_test.py - behavioral/
npz_rip_cog_behav.py , Python, 72 lines - behavioral/
npz_rip_cog_behav_test.p , Python, 29 linesy - get_prad.sh, Shell, 7 lines
- image_masks/
make_DMN.py , Python, 29 lines, 1 match - image_masks/
make_dACC.py , Python, 23 lines - image_masks/
make_subcortical_ROIs.py , Python, 40 lines, 1 match - paths.py, Python, 31 lines
- taskfmri/
0_subjectlist/ , Python, 483 lines, 1 matchinclusions_1.py - taskfmri/
0_subjectlist/ , Python, 90 lines, 1 matchinclusions_1_scanner_inf o_included_family_member .py - taskfmri/
0_subjectlist/ , Python, 35 linesinclusions_control_model s.py - taskfmri/
0_subjectlist/ , Python, 36 linessex.py - taskfmri/
0_subjectlist/ , Python, 112 linessl.py - taskfmri/
0_subjectlist/ , Python, 24 linessl_test.py - taskfmri/
1_preprocess/ , Python, 100 lines, 1 matchim_proc.py - taskfmri/
1_preprocess/ , Shell, 16 linesim_proc.sh - taskfmri/
2_design/ , Python, 659 linesdesign.py - taskfmri/
2_design/ , Python, 83 linesrun_design.py - taskfmri/
2_design/ , Python, 69 linesrun_design_pradG.py - taskfmri/
2_design/ , Python, 69 linesrun_design_pradIR.py - taskfmri/
2_design/ , Python, 67 linesrun_design_rvm.py - taskfmri/
3_individualstats/ , Python, 182 lines, 2 matchesindividualstats.py - taskfmri/
3_individualstats/ , Python, 82 linesrun_individualstats.py - taskfmri/
3_individualstats/ , Python, 88 linesrun_individualstats_oom. py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_prad G.py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_prad IR.py - taskfmri/
3_individualstats/ , Python, 52 linesrun_individualstats_rvm. py - taskfmri/
4_groupstats/ , Python, 617 lines, 1 matchgroupstats.py - taskfmri/
4_groupstats/ , Python, 132 linesgroupstats_one_sample_WB .py - taskfmri/
4_groupstats/ , Python, 75 linesgroupstats_rema.py - taskfmri/
4_groupstats/ , Python, 27 linesprint_n.py - taskfmri/
4_groupstats/ , Python, 58 linesrun_groupstats_one_sampl e_WB.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_pradG.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_pradIR.py - taskfmri/
4_groupstats/ , Python, 53 linesrun_groupstats_one_sampl e_WB_rvm.py - taskfmri/
4_groupstats/ , Jupyter, 50 linessubject_average_mods.ipy nb - taskfmri/
5_more_second_level/ , Jupyter, 108 linesanatomical_nonergodicity .ipynb - taskfmri/
5_more_second_level/ , Jupyter, 475 lines, 2 matchespermutations.ipynb - taskfmri/
5_more_second_level/ , Python, 27 linespermutations.py - taskfmri/
5_more_second_level/ , Python, 151 lines, 1 matchresample.py - taskfmri/
5_more_second_level/ , Python, 98 linesrsa.py - taskfmri/
6_plotting/ , Jupyter, 224 linesanatomical_nonergodicity .ipynb - taskfmri/
6_plotting/ , Jupyter, 336 linescompare_correlations_ds. ipynb - taskfmri/
6_plotting/ , Python, 22 linescompare_correlations_ds_ test.py - taskfmri/
6_plotting/ , Python, 120 linescorrelate_betas_WB.py - taskfmri/
6_plotting/ , Python, 151 lines, 1 matchds_WB.py - taskfmri/
6_plotting/ , Python, 91 linesds_WB_control_models.py - taskfmri/
6_plotting/ , Jupyter, 324 lines, 1 matchoverview.ipynb - taskfmri/
6_plotting/ , Python, 27 lines, 3 matchesplotting_utils.py - taskfmri/
6_plotting/ , Python, 100 linesprint_p_values.py - taskfmri/
6_plotting/ , Python, 112 linesreliability_group.py - taskfmri/
6_plotting/ , Python, 175 linesreliability_individual.p y - taskfmri/
6_plotting/ , Python, 149 linesrema.py - taskfmri/
6_plotting/ , Jupyter, 110 lines, 1 matchresample.ipynb - taskfmri/
6_plotting/ , Jupyter, 257 lines, 1 matchrsa.ipynb - taskfmri/
6_plotting/ , Jupyter, 240 linessubgroups.ipynb - taskfmri/
6_plotting/ , Python, 132 lineswithin_subjects_distribu tions.py - taskfmri/
make_source_data.sh , Shell, 59 lines - taskfmri/
submit_chain.sh , Shell, 21 lines - utilities/
backup_data_to_box.py , Python, 19 lines - utilities/
backup_results_to_box.py , Python, 30 lines - utilities/
parallel.py , Python, 19 lines - utilities/
report_error.py , Python, 32 lines - utilities/
submit.py , Python, 221 lines - README.md, Text, 118 lines
Code availability
All code used in this study has been archived at 10.5281/
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 148 scripts, each with its path and the digest of its content;
- 18 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
Data used in this study were from the ABCD study (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 1, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 3 keywords, 8 MeSH terms, 2 funders, 68 references.
Cite
This paper
Mistry, P. K., Branigan, N. K., Gao, Z., Cai, W., & Menon, V. (2026). Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control. Nature communications, 17(1), 3494. https://
BibTeX
@article{mistry2026noner
author = {Mistry, Percy K and Branigan, Nicholas K and Gao, Zhiyao and Cai, Weidong and Menon, Vinod},
title = {{Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {3494},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/
url = {https://
pmid = {42045209},
pmcid = {PMC13121725}
}
RIS
TY - JOUR
AU - Mistry, Percy K
AU - Branigan, Nicholas K
AU - Gao, Zhiyao
AU - Cai, Weidong
AU - Menon, Vinod
TI - Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/
VL - 17
IS - 1
SP - 3494
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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