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fitKernel

"fitKernel" is a library of matlab functions and scripts to compute Generalized Linear Model (GLM) for cuesaccade data.

Requirement

  • marmodata (loading eye data, needs to be MASTER branch)
  • marmolab-stimuli (loading cuesaccade data)
  • dsbox (ridge regression and some visualization)
  • https://github.com/pillowlab/neuroGLM (GLM fitting)

Environments under linux and windows machines are tested.

Usage

mainScript.m is the main script to to "everything": obtain linear kernel and event-triggered spiking traces

Functions about concatenating trial-based data

  • concatenate_eye: mamordata.eye concatenated across trials
  • concatenate_spk: spike times conctenated across trials
  • decompose_eye: eye data decomposed back into trials from concatenated
  • retrieveTrIdx_r: retrieve temporal indices of every trial from the concatenated data

Main function for kernel estimation

  • fitPSTH_cv: estimate linear kernel with K-fold cross validation using neuroGLM
  • fitPSTH: estimate linear kernel with ridge regression in dsbox (obsolete)
  • fitMultiplicative: (under testing)

Functions about preparing predictor signals

  • processEyeData: main function to concatenate eye data, extract times of saccades, blinks and outliers
  • detectOverlapEvents: detect overlap between the 2nd and 3rd inputs (cf. trace2Event)
  • detectPupilOnsets: start/end times of pupil dilation and constriction according to Einstein 2017 JNS
  • getChoice: times when task outcome is registered (success/failure) of every trial
  • getCueOnset: cue onset times and the task outcome (success/failure) of every trial
  • (getCueDirMtx): matrix of cue direction of all trials (NOT YET FUNCTIONING)
  • getEyeDirMtx: matrix of eye position over time
  • getEyeSpdDirMtx: matrix of eye velocity over time
  • getSaccMtx: matrix of saccade direction over time
  • getTgtDirMtx: matrix of target direction over time
  • getPupilDiameter: converts pupil area into diameter and its percentile
  • getSaccDir: classifies each saccade events into one of quantized bins of directions
  • removeBlinksEDF: eye data after removing times of blinks detected by eyelink
  • removePareaOutliers: eye data after removing times of outliers that crossed a specified threshold
  • selectSaccades: saccade times after eliminating those at specified exclusion periods
  • preparePredictors: matrix of predictors of specified modalities

Functions for analysis/visualization

  • showKernel: shows kernel and predicted PSTH trace over time
  • showSaccOnsetResp: shows observed/predicted PSTH traces triggered by saccade onset OUTSIDE of the task
  • showFixCueOnsetResp: shows observed/predicted PSTH triggered by fixation and cue onsets
  • showTonsetResp: shows observed/predicted PSTH triggered by target and saccade onsets of preferred target direction. Also computes cell class (under development)
  • showTonsetByCue: show observed/predicted PSTH triggered by target onsets with/without cues
  • (dirTuning): preferred direction of spikes at specified time window (TO BE DELETED)
  • (parea_spike_ms): computes correlation between spikes and pupil diameter at specified temporal frequencies
  • (pupilFigure): figure of single-trial traces of pupil position/area and spikes triggered at specified type of events
  • (showPspec_parea_psth NOT CHECKED)
  • (showDirTuning: NOT COMPLETED) : preferred direction of spikes at specified time window
  • modelComparison_test.m : compute Rsquare_adjusted across all the units with getRsqadj.m. Used for JNSS2023
  • getExpVal: computes explained variance of a given period. Called in fitPSTH_cv
  • getExpVal_tgt: computes explained variance after the target stimuli. Called in fitPSTH_pop
  • getExpVal_avgtgt: Called in fitPSTH_pop
  • inclusionCriteria: Called in fitPSTH_pop

Utility functions

  • filtPSTH: (a)causally filtered spike trace
  • alignMtxDir: a matrix which 2nd dimension is rotated based on its preferred direction
  • event2Trace: convert event times into a trace of {0, 1} (cf. trace2Event)
  • trace2Event: converts a trace of {0,1} into event times (cf. Event2Trace)
  • getMonthDateCh: list of datafile names, months, dates and channels saved under rootFolder
  • getPSTH: convert spike times into a trace
  • fitResponse: fit a 1D circular gaussian to single trial data of a given time

Other Analysis Scripts

  • classifyUnits_pop: curates results of showTonsetResp
  • fitPSTH_pop: curates results of fitPSTH_test.m from all neurons and compute statistics
  • parea_spike_ms_test" curates results of parea_spike_ms from all neurons
  • pupilOnsetsResp: spikes(recorded and predicted) triggered by pupil dilation/constriction starts (TOBE MERGED W fitPSTH_test)
  • selectFitPeriod_test: estimate kernel only during fOnset-tOnset (TO BE DELETED)

Note

I don't test environments under Mac.

Author

  • Daisuke Shimaoka

License

fitKernel is confidential.