Tetsuro Funato, Noriaki Hattori, Arito Yozu, Qi An, Tomomichi Oya, Shouhei Shirafuji, Akihiro Jino, Kyoichi Miura, Giovanni Martino, Denise Berger, Ichiro Miyai, Jun Ota, Yury Ivanenko, Andrea d'Avella, and Kazuhiko Seki
Program files (25KB)
Sample Measured Data Files (205.4 MB)
Note: Place "measuredMat" folder in the "sampleMeasuredFiles.zip" to the same folder with program files
("analysis1_synergyExtraction.m" and "analysis2_analysisUsingStadardSynergies.m").
Measured data include one trial data of one healthy subject.
Structure of the sample data files
measuredMat/[trial].mat
mName: Names of Measured Muscles
mFreq: Measurement Frequency
mData: Measured EMG data (42ch). Data in first column are time, and data in each column from second column are time series of EMG data measured from one muscle. The order of muscles are same with the order of muscle names in mName.
measuredMat//taskTime/[trial].csv Initial and end time of each task item
First column: task number
Second column: initial time of the task (MMSS; first two digits represent 'minite' and last two digits represent 'seconds')
Third column: end time of the task (MMSS; first two digits represent 'minite' and last two digits represent 'seconds')
Extraction of muscle synergies from measured EMG data
Usage
1: Calculate VAF using [1,3: Synergy Analysis] function with [calcVAF=1, calcSynergyAll=0]
2: Determine the number of synergies using [2: Evaluation of VAF] functions
3: Calucate Synergies using [1,3: Synergy Analysis] function with [calcVAF=0, calcSynergyAll=1]
1,3: Synergy Analysis function
Calculation of VAF and calculation of Synergies
MATLAB File: analysisEMG.m
[Common Input/Output files]
Input: measuredMat/[trial].mat Measured EMG data (mData) and Name of Muscles (mName)
measuredMat//taskTime/[trial].csv Initial and end time of each task item
Output: resultMat/[Healthy or Stroke]/dataOrig_[trial].mat Measured data after pre-processing
dur[Healthy or Stroke].csv Duration of each task item
[Input/Output files for 1: calcVAF=1]
Output: resultMat/vafAll_[trial].mat
[Input/Output files/Output Figures for 3: calcSynergyAll=1]
Input: resultMat/[Healthy or Stroke]/VAF[VAFThreshold]/synergyNum_VAF[VAFThreshold].mat Number of synergies (pcNum) calculated by [2: Evaluation of VAF]
Output: zAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat Muscle synergies
vAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat Temporal coefficient of muscle synergies
Output Figures: resultFigs/[trial]/emgAnalysis_[Indx].eps
2: Evaluation of VAF
Number of synergies is saved to the file: synergyNum_VAF[VAFThreshold].mat
MATLAB File: evalVAF.m
[Input/Output files]
Input: measuredMat/[trial].mat Measured EMG data (mData) and Name of Muscles (mName)
Output: resultMat/[Healthy or Stroke]/VAF[VAFThreshold]/synergyNum_VAF[VAFThreshold].mat
Output Figures: resultFigs/Healthy/vafAll_subAll.eps VAF of all subjects (Healthy)
resultFigs/Stroke/vafAll_S[subject number].eps VAF of stroke patients (Stroke)
Analyes performed by this program:
Evaluation of standard synergies (1-3)
Merging of Stroke Synergies (4-5)
Severity-merging rate relationship (6)
Usage
Run following programs sequentially by setting their option=1.
1: Calculation of Standard Synergies (synergyGroup.mat) / Draw Fig. 1B, Supplementary Table 3
Calculatoin of Standard Synergies (calcStandardSynergies = 1)
MATLAB File: P1A_calcStandardSynergies.m
[Input/Output files]
Input: zAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat (Synergy of healthy particiapants)
Output: synergyGroup.mat (Standard synergies)
Output Figures: synergyShare[num]_VAF[VAFThreshold].eps (Standard synergies, Fig. 1B)
Evaluate Standard Synergies from muscle area (evalResultsSynEMG=1)
MATLAB File: P1B_evalStandardSynergyFromMuscles
[Input/Output files]
Input : synergyGroup.mat
Output: majorEMGListChOrder_th[threashold].xlsx (Supplementary Table 3)
2: Calculation of temporal coefficient of Healthy/Stroke EMG data corresponding to standard synergies
MATLAB File: P2_calcTCoeff.m
[Input/Output files]
Input: synergyGroup.mat
dataOrig_[trial].mat (EMG file)
Output: wTild_[trial].mat (wTild:temporal coefficient corresponding to standard synergies)
3: Calculate Synergy-Task relationship (Fig. 2)
MATLAB File: P3_calcTaskSynergyRelationship.m
[Input/Output files]
Input: wTilde_[trial].mat
Output: tSynergyTaskList.csv (Healthy) [temporal coeff corresponding to standard synergy is used for evaluation]
tSynergyTaskList_tNum[trial].csv (Stroke) [temporal coeff corresponding to standard synergy is used for evaluation]
tSynergyTaskMildList_tNum[trial].csv (Stroke)
tSynergyTaskSevereList_tNum[trial].csv (Stroke)
Output Figures: synergy-taskTable_VAF[VAFThreshold].eps (Healthy) Fig.2A
synergy-taskTable_Mild_tNum[trial]_VAF[VAFThreshold].eps (Stroke) Supplementary Fig. 4
synergy-taskTable_Severe_tNum[trial]_VAF[VAFThreshold].eps (Stroke) Supplementary Fig. 4
synergy-taskTable_MildDiff_tNum[trial]_VAF[VAFThreshold].eps (Stroke) Fig.2B
synergy-taskTable_SevereDiff_tNum[trial]_VAF[VAFThreshold].eps (Stroke) Fig.2B
Note: Caltulate Healthy using anaProp.tHNum = 0; (Standard Synergy is calculated for all trials)
Caltulate Stroke using anaProp.tHNum = 1 or 2;
4: Calculate Standard Synergy-Stroke Synergy Table (Fig. 3A)
MATLAB File: P4_evalCompStandardStroke.m
[Input/Output files]
Input: synergyGroup.mat
zAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat (Synergy of healthy particiapants)
Output: corrStandardStroke[trial].mat
5: Calulates number of merging stroke synergies (Fig. 3B)
Calcluate merging relationship
MATLAB File: P5A_evalMerging.m
[Input/Output files]
Input: synergyGroup.mat
Output: mergingList_[trial]_VAF[VAFThreshod]_mTh[mergingThreshold].mat (used P5B_summaryMerging.m)
Note: Use this function with anaProp.tHNum = anaProp.tSNum =0
Plot and test results of merging synergies
MATLAB File: P5B_summaryMerging.m
[Input/Output files]
Input: mergingList_[trial]_VAF[VAFThreshod]_mTh[mergingThreshold].mat
Output Figures: numMerging_mTh[mergingThreshold]_tSNum[trial].eps (Fig.3B)
mergingBarsMS_mTh[mergingThreshold]_tHNum[trial]_tSNum[trial]_box.eps (Fig.3B)
6: Calculate Severity-merging rate relationship for each task (Fig. 4AB)
Calculate Synergy-Task relationship of stroke synergies
MATLAB File: P6A_calcTaskStrokeSynergyRelation.m
Input vAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat
Output: tSynergyTaskList2_[trial].csv (Healthy) [temporal coeff corresponding to stroke synergy is used for evaluation]
Calculate number of merging for each task
MATLAB File: P6B_evalMergingTask.m
Input: synergyGroup.mat
zAll_[trial]_pcNum[pcNum]_VAF[VAFThreshold].mat (Synergy of healthy particiapants)
tSynergyTaskList2_[trial].csv
Output: mergeRateTask_mTh[mergingThreshold]_tNum[trial].mat
mergeRateTask_mTh[mergingThreshold]_tNum[trial].xlsx
Output Figures: mergeRateTask_mTh[mergingThreshold]_tNum[trial].eps (Fig. 4A)
Plot p-value list of severity-merge rate relationship for each task
MATLAB File: P6C_summaryMergingTask
Input: mergeRateTask_mTh[mergingThreshold]_tNum[trial].mat
Output Figures: impTaskMergingCVal_mTh[mergingThreshold]_tNum[trial]_VAF[VAFThreshold].eps
impTaskMergingPVal_mTh[mergingThreshold]_tNum[trial]_VAF[VAFThreshold].eps (Fig. 4B)
Following third party matlab functions are required for drawing figures
export_fig
https://jp.mathworks.com/matlabcentral/fileexchange/23629-export_fig
mmpolar
https://jp.mathworks.com/matlabcentral/fileexchange/38855-comprehensive-polar-plots
Following third party matlab functions are required for statistical analysis