Movement Disorder Patients with Depression Have Altered Corticostriatal Alpha-Beta Power Response to Reward and Loss.
The 3 matches
- [1] § Materials and Methods › Neurophysiology and statistical analysis ↔ VerbWM_SecondLevelClusters_permutestref_func.m, lines 1–121 · score 0.70 · shuffled permutations, absolute, randomizations, predictor, sum, matrix
- [2] § Materials and Methods › Neurophysiology and statistical analysis ↔ VerbWMBDIDiagANOVALME.m, lines 88–171 · score 0.56 · linear mixed, way ANOVAs, diagnosis, models, interaction, BDI
- [3] § Materials and Methods › Neurophysiology and statistical analysis ↔ VerbWMBDIDiagANOVALME_OtherVarStats.m, lines 358–420 · score 0.56 · linear mixed, way ANOVAs, diagnosis, models, interaction, BDI
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
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The authors' code
MATLAB · 256 lines · 11 KB · no license · 1 match
- function VerbWM_SecondLevelClusters_permutestref_func(brain_rgn,aligntype,trialtype,data_structure,datatype,subjID,powrange,varargin)
- savename_add=''; % Default is empty
- if ~isempty(varargin)
- for i = 1:2:length(varargin)
- if strcmp(varargin{i},'savename_add')
- savename_add=varargin{i+1};
- end
- end
- end
- % Compute cluster correction threshold
- random_nb=60000; % 60,000 random combinations of all contacts in an ROI, drawn from the 300 shuffles calculated previously for each site
- alpha=0.05;
- % Load data for all subjects
- tMatrix_perm_allsubj=[]; tMatrix_allsubj=[];
- for su=1:length(subjID)
- if strcmp(data_structure,'timefreq')
- if strcmp(datatype,'Power')
- filename=[brain_rgn,'_',aligntype,'_',trialtype,'_',subjID{su},'_FirstLevel_tTest_alldata_Cat'];
- elseif strcmp(datatype,'Bursts')
- filename=[brain_rgn,'_Bursts_',aligntype,'_',trialtype,'_',subjID{su},'_FirstLevel_tTest_alldata_Cat'];
- end
- else
- if strcmp(datatype,'Power')
- filename=[powrange,'_',brain_rgn,'_',aligntype,'_',trialtype,'_',subjID{su},'_FirstLevel_tTest_alldata_Cat'];
- elseif strcmp(datatype,'Bursts')
- filename=[powrange,'_',brain_rgn,'_Bursts_',aligntype,'_',trialtype,'_',subjID{su},'_FirstLevel_tTest_alldata_Cat'];
- end
- end
- tempload = load(filename);
- tMatrix_perm_ch=tempload.tMatrix_perm_ch;
- tMatrix_ch=tempload.tMatrix_ch;
- for ch=1:length(tMatrix_perm_ch)
- % For shuffled permutations: Concatenate frequency x time x permutation x channel matrix
- tMatrix_perm_allsubj = cat(4,tMatrix_perm_allsubj,tMatrix_perm_ch{ch});
- % For non-shuffled: Concatenate frequency x time x channel matrix
- tMatrix_allsubj = cat(3,tMatrix_allsubj,tMatrix_ch{ch});
- end
- clear tempload
- end
- permstat_correct = NaN(random_nb, 1); % Initialization (randomizations x 1), original code had it as randomizations x 1 x number of predictors (which is just 1 in our case)
- % Randomization loop
- tic
- parfor rd = 1:random_nb
- disp(['Randomization # ',num2str(rd)]); tic
- h_matrix = NaN(size(tMatrix_perm_allsubj,1),size(tMatrix_perm_allsubj,2)); % Initialize frequency x time matrix
- t_matrix = NaN(size(tMatrix_perm_allsubj,1),size(tMatrix_perm_allsubj,2)); % Initialize frequency x time matrix
- for ff=1:size(tMatrix_perm_allsubj,1)
- rd_perm = NaN(size(tMatrix_perm_allsubj,4),size(tMatrix_perm_allsubj,2)); % Initialize (channels x time)
- for chan = 1:size(tMatrix_perm_allsubj,4) % Loop over channels
- ichan = randperm(size(tMatrix_perm_allsubj,3), 1); % We take a random permutation for each contact
- rd_perm(chan,:) = squeeze(tMatrix_perm_allsubj(ff, :, ichan, chan)); % Channel x Time
- end
- % MATLAB default is two-tailed test w/ alpha of 0.05
- [h,~,~,stats] = ttest(rd_perm); % T-test (over channels, returns a t-value for each time index)
- h_matrix(ff,:)=h;
- t_matrix(ff,:)=stats.tstat;
- end
- h=[]; stats=[];
- % Compute t-value threshold from p-value threshold (two-sided, dependent samples)
- num_channels = size(tMatrix_perm_allsubj,4);
- tThreshold = abs(tinv((1-alpha/2), num_channels-1)); %using total N-1 number of channels for DF
- % Find positive clusters (must be done separately in case positive and
- % negative clusters are connected)
- pos_t_idx = find(t_matrix > tThreshold);
- pos_h_matrix = zeros(size(h_matrix));
- pos_h_matrix(pos_t_idx) = 1;
- L_pos = spm_bwlabel(pos_h_matrix); %% Find clusters (number indices of each identified cluster with a number)
- % Find negative clusters
- neg_t_idx = find(t_matrix < -tThreshold);
- neg_h_matrix = zeros(size(h_matrix));
- neg_h_matrix(neg_t_idx) = 1;
- L_neg = spm_bwlabel(neg_h_matrix); %% Find clusters (number indices of each identified cluster with a number), includes both negative and positive clusters
- % Analyze all clusters (numbered in L)
- clusternum_pos = max(L_pos,[],'all'); % Count positive clusters
- clusternum_neg = max(L_neg,[],'all'); % Count negative clusters
- stats_summary_pos = NaN(clusternum_pos,1); % Initialization
- stats_summary_neg = NaN(clusternum_neg,1); % Initialization
- stats_summary_tmp = [];
- for k = 1:clusternum_pos % Positive clusters
- stats_summary_pos(k,:) = sum(t_matrix(L_pos==k)); % Sum t-values of cluster
- end
- for k = 1:clusternum_neg % Negative clusters
- stats_summary_neg(k,:) = sum(t_matrix(L_neg==k)); % Sum t-values of cluster
- end
- stats_summary_tmp = [stats_summary_pos;stats_summary_neg];
- % Fill the cluster matrix
- if isempty(stats_summary_tmp) % There is no cluster
- permstat_correct(rd) = 0;
- else % Find the biggest cluster
- [~,max_idx] = max(abs(stats_summary_tmp));
- permstat_correct(rd) = abs(stats_summary_tmp(max_idx)); % Sum t-values of the biggest cluster
- % Storing absolute value of t-value sum for ease of use of permstat_correct
- % to get absolute threshold from percentile function
- end
- toc;
- end
- toc
- %% Non-shuffled statistics
- % Loop over frequencies
- h_matrix = NaN(size(tMatrix_allsubj,1),size(tMatrix_allsubj,2)); % Initialize frequency x time matrix
- t_matrix = NaN(size(tMatrix_allsubj,1),size(tMatrix_allsubj,2)); % Initialize frequency x time matrix
- avg_tMatrix = NaN(size(tMatrix_allsubj,1),size(tMatrix_allsubj,2)); % Initialize frequency x time matrix
- for ff=1:size(tMatrix_allsubj,1)
- avg_tMatff = squeeze(mean(tMatrix_allsubj(ff,:,:),3,'omitnan')); % Keep time course, average t-values over channels
- [h,~,~,stats] = ttest(squeeze(tMatrix_allsubj(ff,:,:))'); % T-test (over channels, returns a t-value for each time index)
- h_matrix(ff,:)=h;
- t_matrix(ff,:)=stats.tstat;
- avg_tMatrix(ff,:)=avg_tMatff;
- end
- h=[]; stats=[];
- % Compute t-value threshold from p-value threshold (two-sided, dependent samples)
- num_channels = size(tMatrix_allsubj,3);
- tThreshold = abs(tinv((1-alpha/2), num_channels-1)); %using total N-1 number of channels for DF
- % Find positive clusters (must be done separately in case positive and
- % negative clusters are connected)
- pos_t_idx = find(t_matrix > tThreshold);
- pos_h_matrix = zeros(size(h_matrix));
- pos_h_matrix(pos_t_idx) = 1;
- L_pos = spm_bwlabel(pos_h_matrix); %% Find clusters (number indices of each identified cluster with a number)
- % Find negative clusters
- neg_t_idx = find(t_matrix < -tThreshold);
- neg_h_matrix = zeros(size(h_matrix));
- neg_h_matrix(neg_t_idx) = 1;
- L_neg = spm_bwlabel(neg_h_matrix); %% Find clusters (number indices of each identified cluster with a number), includes both negative and positive clusters
- %% Cecchi verson of p-threshold
- % Count all clusters (numbered in L)
- clusternum_pos = max(L_pos,[],'all'); % Count positive clusters
- clusternum_neg = max(L_neg,[],'all'); % Count negative clusters
- clusternum_tot = clusternum_pos + clusternum_neg;
- % Initialization
- stats_summary_pos = cell(clusternum_pos,3);
- stats_summary_neg = cell(clusternum_neg,3);
- clusteridx_store = {};
- mean_tVal=[];
- t_stat_sig=[]; p_val_sig=[]; % Initialization of cluster statistics
- % Positive clusters
- for k = 1:clusternum_pos % Analyze all clusters (numbered in L_pos)
- stats_summary_pos{k,1} = mean(avg_tMatrix(L_pos == k)); % (1) Mean of cluster
- if strcmp(data_structure,'bandavg')
- time_idx = find(L_pos == k); % Get cluster time indices
- stats_summary_pos{k,2} = time_idx; % (2) Cluster indices
- else
- [row_idx,col_idx] = find(L_pos == k); % Get 2D cluster indices
- stats_summary_pos{k,2} = [row_idx,col_idx]; % (2) Cluster indices
- end
- stats_summary_pos{k,3} = sum(t_matrix(L_pos == k)); % (3) Sum of t-values of cluster
- if ~isempty(permstat_correct) % Permutation correction
- abs_thresh = prctile(permstat_correct(:, 1), 100-(alpha/clusternum_tot)*100); % Bonferroni correct for number of clusters
- if abs(stats_summary_pos{k,3}) > abs_thresh % Cluster significant
- t_stat_sig(end+1) = stats_summary_pos{k,3}; % Sum t-values of cluster
- randgreater_count = length(find(permstat_correct(:,1) > abs(stats_summary_pos{k,3})));
- p_val_sig(end+1) = (randgreater_count+1) / (length(permstat_correct(:,1))+1);
- clusteridx_store{end+1} = stats_summary_pos{k,2};
- mean_tVal(end+1) = stats_summary_pos{k,1};
- end
- else % No correction
- disp('No correction, empty permstat_correct')
- end
- end
- % Negative clusters
- for k = 1:clusternum_neg % Analyze all clusters (numbered in L_neg)
- stats_summary_neg{k,1} = mean(avg_tMatrix(L_neg == k)); % (1) Mean of cluster
- if strcmp(data_structure,'bandavg')
- time_idx = find(L_neg == k); % Get cluster time indices
- stats_summary_neg{k,2} = time_idx; % (2) Cluster indices
- else
- [row_idx,col_idx] = find(L_neg == k); % Get 2D cluster indices
- stats_summary_neg{k,2} = [row_idx,col_idx]; % (2) Cluster indices
- end
- stats_summary_neg{k,3} = sum(t_matrix(L_neg == k)); % (3) Sum of t-values of cluster
- if ~isempty(permstat_correct) % Permutation correction
- abs_thresh = prctile(permstat_correct(:, 1), 100-(alpha/clusternum_tot)*100); % Bonferroni correct for number of clusters
- if abs(stats_summary_neg{k,3}) > abs_thresh % Cluster significant
- t_stat_sig(end+1) = stats_summary_neg{k,3}; % Sum t-values of cluster
- randgreater_count = length(find(permstat_correct(:,1) > abs(stats_summary_neg{k,3})));
- p_val_sig(end+1) = (randgreater_count+1) / (length(permstat_correct(:,1))+1);
- clusteridx_store{end+1} = stats_summary_neg{k,2};
- mean_tVal(end+1) = stats_summary_neg{k,1};
- end
- else % No correction
- disp('No correction, empty permstat_correct')
- end
- end
- % Sort clusters in order of significance
- [t_stat_sig_sort,sort_idx] = sort(abs(t_stat_sig),'descend');
- p_val_sig_sort = p_val_sig(sort_idx);
- sig_clusters = clusteridx_store(sort_idx);
- mean_tVal_sort = mean_tVal(sort_idx);
- if strcmp(data_structure,'timefreq')
- if strcmp(datatype,'Power')
- SaveName=[brain_rgn,'_',aligntype,'_',trialtype,'_Clusters_permutestref_Cecchi',savename_add];
- elseif strcmp(datatype,'Bursts')
- SaveName=[brain_rgn,'_Bursts_',aligntype,'_',trialtype,'_Clusters_permutestref_Cecchi',savename_add];
- end
- else
- if strcmp(datatype,'Power')
- SaveName=[powrange,'_',brain_rgn,'_',aligntype,'_',trialtype,'_Clusters_permutestref_Cecchi',savename_add];
- elseif strcmp(datatype,'Bursts')
- SaveName=[powrange,'_',brain_rgn,'_Bursts_',aligntype,'_',trialtype,'_Clusters_permutestref_Cecchi',savename_add];
- end
- end
- save(SaveName,'t_stat_sig_sort','p_val_sig_sort','sig_clusters','mean_tVal_sort','avg_tMatrix','clusternum_tot');
- end
VerbWM_SecondLevelClusters_permutestref_func.m at commit 63e6cc6, no license · at the source
Overview
- Harvard Medical School, Boston, Massachusetts 02115
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee 37212
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, Tennessee 37232
- Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota 55905
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Neurosurgery, Henry Ford Hospital, Detroit, Michigan 48202
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Geriatric Research, Education and Clinical Center (GRECC), Tennessee Valley Healthcare System Veterans Administration, Nashville, Tennessee 37212
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, Texas 75390
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37212
Abstract
Depression is a common comorbidity in movement disorders such as Parkinson's disease (PD) and essential tremor (ET). Altered reward signaling contributes to core depression symptoms such as anhedonia, but the specific neural activity patterns underlying these processes and how they manifest in comorbid movement disorders are incompletely understood. Fourteen PD and 16 ET patients (22 male, 8 female) participated while undergoing deep brain stimulation surgery. Subjects completed a working memory task and received visual feedback about response accuracy while signals were recorded from traversed structures [caudate and/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.
qhelen/MD-Depression-Reward
63e6cc66e3584bd1558aed55d1f3968f9c509b56, 9 January 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
9 files
- VerbWMBDIDiagANOVALME.m, MATLAB, 171 lines, 1 match
- VerbWMBDIDiagANOVALME_Ot
herVarStats.m , MATLAB, 420 lines, 1 match - VerbWMBaselineStatsV4.m, MATLAB, 469 lines
- VerbWMCorrVIncorrVBaseli
ne_SignificantChannels.m , MATLAB, 679 lines - VerbWMDepressionOtherVar
Stats.m , MATLAB, 880 lines - VerbWMFirstLevelClusters
_tTest.m , MATLAB, 138 lines - VerbWMNeuroPsychTaskPlot
.m , MATLAB, 176 lines - VerbWMSecondLevelCluster
sCallContainer.m , MATLAB, 44 lines - VerbWM_SecondLevelCluste
rs_permutestref_func.m , MATLAB, 256 lines, 1 match
Code accessibility
The code/
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.
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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.
Versions
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 6 keywords, 17 MeSH terms, 2 funders, 59 references.
Cite
This paper
Qian, H., Johnson, G. W., Hughes, N. C., Chao, A., Long, I. C., Paulo, D. L., Zhao, Z., Subramanian, D., Taylor, W. D., Dhima, K., & Bick, S. K. (2026). Movement Disorder Patients with Depression Have Altered Corticostriatal Alpha-Beta Power Response to Reward and Loss. eNeuro, 13(7), ENEURO.0008-26.2026. https://
BibTeX
@article{qian2026movemen
author = {Qian, Helen and Johnson, Graham W. and Hughes, Natasha C. and Chao, Astoria and Long, Isabel C. and Paulo, Danika L. and Zhao, Zixiang and Subramanian, Deeptha and Taylor, Warren D. and Dhima, Kaltra and Bick, Sarah K.},
title = {{Movement Disorder Patients with Depression Have Altered Corticostriatal Alpha-Beta Power Response to Reward and Loss}},
journal = {eNeuro},
year = {2026},
month = jul,
volume = {13},
number = {7},
pages = {ENEURO.0008--26.2026},
publisher = {Society for Neuroscience},
issn = {2373-2822},
doi = {10.1523/
url = {https://
pmid = {42386530},
pmcid = {PMC13364504}
}
RIS
TY - JOUR
AU - Qian, Helen
AU - Johnson, Graham W.
AU - Hughes, Natasha C.
AU - Chao, Astoria
AU - Long, Isabel C.
AU - Paulo, Danika L.
AU - Zhao, Zixiang
AU - Subramanian, Deeptha
AU - Taylor, Warren D.
AU - Dhima, Kaltra
AU - Bick, Sarah K.
TI - Movement Disorder Patients with Depression Have Altered Corticostriatal Alpha-Beta Power Response to Reward and Loss
T2 - eNeuro
J2 - eNeuro
PY - 2026
DA - 2026/
VL - 13
IS - 7
SP - ENEURO.0008
EP - 26.2026
SN - 2373-2822
PB - Society for Neuroscience
DO - 10.1523/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1523/
"type": "article-journal",
"title": "Movement Disorder Patients with Depression Have Altered Corticostriatal Alpha-Beta Power Response to Reward and Loss",
"container-title": "eNeuro",
"author": [
{
"family": "Qian",
"given": "Helen"
},
{
"family": "Johnson",
"given": "Graham W."
},
{
"family": "Hughes",
"given": "Natasha C."
},
{
"family": "Chao",
"given": "Astoria"
},
{
"family": "Long",
"given": "Isabel C."
},
{
"family": "Paulo",
"given": "Danika L."
},
{
"family": "Zhao",
"given": "Zixiang"
},
{
"family": "Subramanian",
"given": "Deeptha"
},
{
"family": "Taylor",
"given": "Warren D."
},
{
"family": "Dhima",
"given": "Kaltra"
},
{
"family": "Bick",
"given": "Sarah K."
}
],
"container-title-short":
"volume": "13",
"issue": "7",
"page": "ENEURO.0008-26.2026",
"DOI": "10.1523/
"PMID": "42386530",
"PMCID": "PMC13364504",
"ISSN": "2373-2822",
"publisher": "Society for Neuroscience",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
13
]
]
}
}
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