Input argument reference

CGM inputs arguments

Calibration

Add the -h to the command (e.g. pycgm2.exe NEXUS CGM1.0 Calibration -hcopy) to know the input arguments of the CGM1.0 calibration process ( replace CGM1.0copy for other CGM )

example 1

pycgm2.exe NEXUS CGM1.0 Calibration -l 0 -r 1 -md 16 --check
copy

or

pycgm2.exe NEXUS CGM1.0 Calibration --leftFlatFoot 0 --rightFlatFoot 1 --markerDiameter 16 --check
copy

=> disable the left flat foot option, keep enable the right flat foot option, use 16mm marker diameter and add the suffix _cgm1 to model ouputs

example 2

pycgm2.exe NEXUS CGM2.1 Calibration -forceLHJC 30 50 60
copy

=> position the left hip joint centre relative to the pelvic coordinate system with the coodinates 30 50 and 60

This table resumes all available arguments across CGM

CGMlong optionsshort optionsTypeDescription
CGM1.0+--leftFlatFootcopy-lintcopyLeft flat foot option
CGM1.0+--rightFlatFootcopy-rintcopyRight flat foot option
CGM1.0+--headFlatcopy-hfcopyintcopyHead flat option
CGM1.0+--markerDiametercopy-mdcopyfloatcopyMarker diameter
CGM1.0+--pointSuffixcopy-pscopystrcopySuffix of the model outputs
CGM1.0+--checkcopyForce cgm version as model output suffix
CGM1.0+--resetMPcopyReset the optional anthropometric parameters
CGM1.0+--forceMPcopyForce the use of the MP offsets to compute knee and ankle joint centres
CGM1.0+--anomalyExceptioncopy-aecopyRaise an exception if an anomaly is detected
CGM1.0+--offlinecopynargs=2copyoffline mode, need the subject name and the static c3d filename
CGM2.1+--forceLHJCcopynargs=3copyForce the position of the left hip joint centre to respect local position into the pelvic coordinate system
CGM2.1+--forceRHJCcopynargs=3copyForce the position of the right hip joint centre to respect local position into the pelvic coordinate system
CGM2.2 and 2.3--musculoSkeletalModelcopy-msmcopyenable Musculoskeletal computation
CGM2.3+--noIkcopydisbale kinematic fitting ( aka inverse kinematics)

Fitting

Add the -h to the command (e.g. pycgm2.exe NEXUS CGM1.0 Fitting -hcopy) to know the input arguments of the CGM1.0 calibration process ( replace CGM1.0copy for other CGM )

example 1

pycgm2.exe NEXUS CGM1.0 Fitting -md 16 --proj Proximal --pointSuffix test
copy

=> use 16mm marker diameter, project moment into the proximal coordinate system and add the suffix _test to model ouputs

This table resumes all available arguments across CGM

CGMlong optionsshort optionsTypeDescription
CGM1.0+--markerDiametercopy-mdcopyfloatcopyMarker diameter
CGM1.0+--pointSuffixcopy-pscopystrcopySuffix of the model outputs
CGM1.0+--checkcopyForce cgm version as model output suffix
CGM1.0+--anomalyExceptioncopy-aecopyRaise an exception if an anomaly is detected
CGM1.0+--offlinecopynargs=3copyoffline mode, need the subject name and the gait c3d filename and the foot force plate assignment
CGM1.0+--frameInitcopy-ficopyintcopyinitial frame to process
CGM1.0+--frameEndcopy-fecopyintcopylast frame to process
CGM1.0+--projcopystrcopyReferential to project joint moment (choice : Distal,Proximal,Global (and JCS for CGM1.1+))
CGM2.2 and 2.3--musculoSkeletalModelcopy-msmcopyenable Musculoskeletal computation
CGM2.3+--accuracycopy-afloatcopyinverse kinematic solver accuracy ()
CGM2.3+--noIkcopystore_truecopydisbale kinematic fitting ( aka inverse kinematics)

CGM2.6

Depending your functional knee calibration method, type pycgm2.exe NEXUS CGM2.6 2DOF -hcopy) or pycgm2.exe NEXUS CGM2.6 SARA -hcopy to know the input arguments

pycgm2.exe NEXUS CGM2.6 SARA -fi 300 -fe 600 --side Right
copy

=> calibrate the right knee from frame 300 to 600

for both methods, the input arguments are

long optionsshort optionsTypeDescription
--sidecopy-sstrcopybody side ( Left or Right)
--frameInitcopy-ficopyintcopyinitial frame to process
--frameEndcopy-fecopyintcopylast frame to process

Events

Zeni et al 2008 - gait event detection

pycgm2.exe NEXUS Events Zeni -fso 5
copy

=> add an offset of 5 to all detected foot strike

long optionsshort optionsTypeDescription
--footStrikeOffsetcopy-fsocopyintcopysystematic foot strike offset on both side
--footOffOffsetcopy-foocopyintcopysystematic foot off offset on both side

Plots

Spatio temporal plots

pycgm2.exe NEXUS Plots STP -ps test
copy

=> build panel from spatiotemporal variables suffixed test

long optionsshort optionsTypeDescription
--pointSuffixcopy-pscopystrcopyconsider model outputs with the given suffix

Kinematics and kinetics - Temporal plot

pycgm2.exe NEXUS Plots Kinematics Temporal -ps test
pycgm2.exe NEXUS Plots Kinetics Temporal -ps test
copy

=> build panel from model ouputs suffixed test

long optionsshort optionsTypeDescription
--pointSuffixcopy-pscopystrcopyconsider model outputs with the given suffix

Kinematics and kinetics - Time-normalized and Comparison Panels

Time-normalized and Comparison panels share similar arguments

type NEXUS Plots Kinematics Normalized -hcopy or NEXUS Plots Kinematics Comparison -hcopy to know the input arguments ( idem with Kineticscopy)

pycgm2.exe NEXUS Plots Kinematics Normalized --consistency -ps test -nd Schwartz2008 -ndm VerySlow
pycgm2.exe NEXUS Plots Kinematics Comparison --consistency -ps test -nd Schwartz2008 -ndm VerySlow
copy

=> build kinematic panel from model ouputs suffixed test. the panel render all cycles rather the average and the std corridor. the panel also call the modality Very slow of the open normative dataset from Schwartz2008

long optionsshort optionsTypeDescription
--consistencycopy-creturn consistency trace ( ie all cycles)
--pointSuffixcopy-pscopystrcopyconsider model outputs with the given suffix
--normativeDatacopy-ndcopystrcopynormative Data set (Schwartz2008 or Pinzone2014)
--normativeDataModalitycopy-ndmcopystrcopyif Schwartz2008 [VerySlow,Slow,Free,Fast,VeryFast] - if Pinzone2014 [CentreOne,CentreTwo]

EMG - Temporal plots

type NEXUS Plots EMG Temporal -hcopy to know the input arguments

pycgm2.exe NEXUS Plots EMG Temporal --raw -bpf 200 400 
copy

=> render non-rectified emg channels. The process applies a bandpass filter [200-400Hz]

long optionsshort optionsTypeDescription
--BandpassFrequenciescopy-bpfcopybandpass frequencies
--EnvelopLowpassFrequencycopy-elfcopyenvelop lowpass cutoff frequency
--rawcopy-rreturn non-rectified values
--ignoreNormalActivitycopy-inacopydo not display normal activity area in the back ground

EMG - Time-normalized and Comparison Panels

type NEXUS Plots EMG Normalized -hcopy or NEXUS Plots EMG Comparison -hcopy to know the input arguments

pycgm2.exe NEXUS Plots EMG Normalized --consistency -bpf 200 400 -elp 8.9
copy

=> render all cycles instead of the average and the std corridor. the process applies a bandpass filter [200-400Hz] and construct the emg envelop with a cut-off frequency of 8.9

long optionsshort optionsTypeDescription
--BandpassFrequenciescopy-bpfcopybandpass frequencies
--EnvelopLowpassFrequencycopy-elfcopyenvelop lowpass cutoff frequency
--consistencycopy-creturn consistency traces ( ie all cycles)