Code related to fUSi rig and fUSi data analysis
ExpRef - Unique experiment reference for the y-stack acquisition ('structural' stack of the whole accessible brain usually
acquired once per experiment)
xAxis - a vector of x coordinates in mm (along the ultrasound probe) of the pixels/voxels in the Doppler data
zAxis - a vector of z coordinates in mm (away from the ultrasound probe - depth) of the pixels/voxels in the Doppler data
yAxis - a vector of y coordinates in mm - position of the motor, which is moving the probe in the direction approximately
orthogonal to a single x-z plane
boundingBox - a structure with information about the useful range of x, y, and z coordinates - used for cropping data
mask - additional mask (polygon) used to define non-rectangular region of interest for analysis -
area outside of this mask will be 'zeroed' in the subsequent analyses
Doppler - nZ-by-nX-by-nY array with the 'structural' brain image - useful for 3-D alignment across sessions, across animals, and to the atlas
BMode - structural data acquired using B-Mode of ultrasound. Because of low ultrasoung contrast in the brain, not really useful
fusi - an array of Fus objects (functional data) associated with the current YStack object
svd - spatial components of the SVD decomposition (if was performed) of the original data (U and S of the [U, S, V] = svds(doppler, nSVDs))
svdReg - spatial components of the SVD decomposition (if was performed) of the registered data
regParams - parameters used for registration (if performed by a proper method of YStack class)
YStack
addFus
addlistener
applyMask
autoCrop
exportStruct
getDoppler
getMask
getOutliers
getRetinotopy
getdII
manualCrop
plotSVDs
plotSlices
plotVolume
plotVolumeMultiple
processFastDoppler
regDoppler
renderVolumeRotation
rotateUdII
saveLite
svdDecomposition
svddII
ExpRef - unique experiment reference
yStack - handle to the associated YStack
doppler - functional Doppler data - nZ-by-nX-by-nT
dopplerFast - fast functional Doppler data - temporally subdivided doppler, average of N dopplerFast frames is equal to a single doppler frame
regDoppler - registered doppler
regDopplerFast - registered dopplerFast
xAxis - x coordinates (in mm) of doppler and dopplerFast data. Can be different to the xAxis property of the associated YStack if the functional data is already cropped.
zAxis - z (depth) coordinates (in mm) of doppler and dopplerFast data. Can be different to the zAxis property of the associated YStack if the functional data is already cropped.
yCoord - the y coordinate in mm of the slice from YStack where the functional data was acquired
tAxis - timestamps of onsets of doppler frames
tAxisFast - timestamps of onsets of dopplerFast frames
dt - duration of the doppler frame ('exposure time'). Important to note - this is not a usual sampling time, as in this system the sampling might not be uniform
dtFast - duration of the dopplerFast frame. Also, read the note in dt property above
protocol - mpep experimental protocol file (TODO explanation on mpep required here, but this is a long topic)
block - block file generated by expServer (for MC experiments, more information might be available here https://github.com/cortex-lab/Rigbox at some point)
pars - stimulus parameters (the exact contents depends on what experiment was performed)
TL - Timeline structure (Timeline is part of https://github.com/cortex-lab/Rigbox)
hwInfo - hardware information (mostly about the visual stimulus apparatus)
stim - a preprocessed protocol to make more sence of the stimuli presented, might not always be correctly preprocessed, needs manual verification
stimTimes - timestamps of stimulus presentations. The exact format depends on the type of experiment performed, but in general will have stimulus onset and offset times (not individual frames)
stimFrameTimes - for mpep expeiments only - times of individual frames (textures in stim) acquired by a photodiode attached to the monitor and reading the 'sync square'
stimSequence - for MC experiments only - the sequence of stimuli (what contrast, azimuth, amplitude etc. was the stimulus on every trial). Exact structure depends on the experiment type. Should be used together with stimTimes
eyeMovie - VideoReader object of the eye-tracking movie
eyeTimes - timestamps of the frames of the eyeMovie
The following properties will only be populated after additional analyses:
outlierFrameIdx - doppler frames identified as outliers (usually due to motion artifacts)
outlierFrameIdxFast - dopplerFast frames identified as outliers (usually due to motion artifacts)
dII - dI/I0 of doppler
dIIFast - dI/I0 of dopplerFast
regDII - dI/I0 of regDoppler
regDIIFast - dI/I0 of regDopplerFast
retinotopyMaps - retinotopy maps calculated form doppler (or regDoppler if registration was performed)
retinotopyMapsFast - retinotopy maps calculated form dopplerFast (or regDopplerFat if registration was performed)
svd - temporal components of the SVD decomposition (V from the [U, S, V] = svds(doppler, nSVDs)) of the original doppler and dopplerFast
svdReg - temporal components of the SVD decomposition of the registered regDoppler and regDopplerFast
D - estimated displacement fields used for registration (see also MATLAB's imregdemons())
Fus
addlistener
dIIMovie
getCroppedDoppler
getETA
getOutliers
getRetinotopy
getdII
hardCrop
movie
projectFastDoppler
regFastDoppler
showRetinotopy