This is a collection of MATLAB utilities developed by Kendrick Kay ([email protected], http://kendrickkay.net). The philosophy of the code is to maximize power (i.e. the ability to perform many different things) and generality (i.e. the ability to re-use code for many different situations). Let me know if you have comments.

Some of the code uses random-number generation, so it is recommended that you have something like

rand('state',sum(100*clock));

randn('state',sum(100*clock));

in your MATLAB startup.m file.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CHANGE HISTORY

Below we document major code changes. Minor code changes and tweaks that have no significant impact are not mentioned here (e.g. things like cosmetic adjustments, code speed-ups, making functions more general by adding optional input arguments, fixing bugs that would have result in code crashes, etc.). Major changes include things that make the code backwards-incompatible and things that change actual analysis results.

History of major code changes:

2019/09/23 - major bug fix to matchfiles.m. previously the order of cell vector elements was not respected. now order is respected.

2018/12/22 - matchfiles.m now RETURNS any duplicate filename matches. This changes past behavior.

2018/12/22 - to resolve function naming conflicts, we have done the following: (1) completely removed the function called count.m, (2) completely removed the function called discretize.m, (3) renamed the function strsplit.m to strsplitalt.m

2014/07/31 - in constructpolynomialmatrix.m, we now make the polynomials orthogonal and unit length. this changes previous behavior!

2013/11/18 - use a smoother canonical HRF in getcanonicalhrf.m

2013/09/07 - fix bug in fitnonlinearmodel (if polynomials or extra regressors were used in multiple runs, then they were not getting fit properly).

2013/08/18 - in makedirid.m, occurrences of '-' are now replaced with '_'

2013/08/18 - in projectionmatrix.m, in the cases of empty <X>, we now return 1 instead of [].

2012/06/14 - in constructpolynomialmatrix2d.m and constructpolynomialmatrix3d.m, we now sort the char representation of the basis functions. the reason is that previously, different machine architectures would give different orders for the basis functions. this is horrible, as it means that different machines would have different parameter orders. the fix (which hopefully is robust) is to sort the basis function character-wise, explicitly. please be aware of this change!

2012/01/23 - in viewimage.m, no longer make a new window and no longer return the figure number

2011/12/10 - in applymultiscalegaussianfilters.m, we now make the default mode to be 0 (center on pixels). this changes previous behavior.

2011/10/13 - in pton.m, now always generate a CLUT at 8-bit (256 rows)

2011/10/09 - in fitprfstatic.m, <outputfcn> no longer accepts all those special inputs; it is now a usual OutputFcn.

2011/09/22 - add required argument to copyxform_nii

2011/09/16 - the default behavior in dicomloaddir has changed. we now match all files and perform numerical sorting.

2011/09/13 - make the yellow color in cmapdistinct slightly darker

2011/08/30 - in fitprf.m, we now use stepwise fitting in the nonlinear case (i.e. <mode> is not 0 nor {0}). this should improve the avoidance of local minima problems, but does change previous behavior!!

2011/07/11 - in dicomloaddir.m, we now have the extra assumption that all files are DICOM files when <filenameformat> is supplied

2011/07/01 - we now use nanmedian and nanmean in calcmdse.m

2011/06/29 - in printnice.m, we now temporarily change PaperPositionMode to auto before printing. this should make rasterized image output better (in terms of getting the resolution right).

2011/06/27 - in olsmatrix.m, we now explicitly handle the case of all-zero regressors. previously, NaNs would result. now, we just ensure that these all-zero regressors get returned a zero weight.

2011/05/26 - in scatterb.m, we weren't drawing the main line. weird. we have changed it now to do the right thing. this modifies old behavior.

2011/04/26 - in constructorientationfilter.m, fixed major bug. orientation was interpreted wrongly and filters were peaked at the wrong orientation.

2011/04/02 - in matchfiles.m, time-sorting behavior did not work (it would always give alphabetical order). fixed now.

2011/03/09 - in defineellipse3d.m, we now show a maximum of 25 slices.

2011/03/08 - for alignvolumedata.m, make much faster (using ba_interp3), take less memory, remove spline interpolation option, ensure that the alignvolumedata_auto_outputfcn runs at optimization completion.

2011/03/08 - smoothvolumes handles NaNs intelligently now. this changes old behavior.

2011/03/06 - complete revamp of calcnoiseceiling.m.

2011/02/24 - in matchfiles.m, we now properly match patterns that have spaces in them (since we now escape the spaces using \). previous behavior was to simply not match those cases.

2011/02/02 - in zerodiv.m, in the case that y is not a scalar and wantcaution is set to 0, we were allowing division by 0 to result in Inf and *notreplaced with val as desired. big mistake. we have now fixed this. utilities that could have used this buggy behavior of zerodiv include calccod, calccorrelation, calcentropy, calcsparseness, calczscore, l1unitlength, unitlength.

2011/01/21 - in matchfiles.m, we explicitly use MATLAB's sort function (for alphabetical ordering) to ensure consistency across platforms. this might change the alphabetical ordering of matches!

2010/01/17 - completely change cmapdistinct.m; leave JVM on by default in runmatlabinbg.pl

2010/01/05 - in scatterline.m, we now attempt to use nanmean and nanstd to allow more cases in. see code for details.

2010/12/27 - in divnorm.m, we now explicitly handle cases where the numerator is Inf. the goal is to try to keep outputs finite when possible.

2010/12/16 - circlewithin.m changed from binary (all within or not) to a graded response

2010/12/06 - in fitprf.m, change initial seeds for certain basis function cases (in particular, we no longer force weights to 1. it seems that nonlinear fitting can operate successfully even if there is a gain ambiguity)

2010/12/03 - in fitprf.m, changed the form of the input <hrfnormfun> (this requires changes to how the function is called);

2010/12/02 - in fitprf.m and fitprfmulti.m, a number of significant changes: [<ar> input has been deprecated; <arfile> input has been removed; the <meanint>,<driftstd>,<signalrms>,<noiserms> outputs have been removed (I no longer think they are useful); fix bug --- the signal and drift outputs were not getting assigned in the re-do calls of the [A B C] case of <maxiter>]; removed evaluateprfmodel.m

2010/11/24 - remove hrfsample1, remove hrfsample2 [these were obsolete]

2010/11/23 - in calccod.m, change the output range to percentages (R^2). thus the range is (-Inf,100]. also, we removed the <wantr> input since it was dumb. also, please note that many functions that rely on calccod.m inherit this change to percentages. thus, this was a big global code change.

2010/10/24 - we now impose assumption in rowfun.m that each result has the same size

2010/10/22 - in fitprf.m, fix bug concerning exitflag and maxiters. if there were multiple resamplings, then we were checking only the last exitflag when deciding to re-do the fitting process. now, we do the right thing --- we check to see if any of the resamplings stopped because they reached the max number of iterations.

2010/10/22 - in fitprf.m, change initial seed for prfmodel and hrfmodel basis functions to 0!

2010/10/09 - remove showmulticlass.m

2010/10/05 - fixed bugs in sortnumerical.m. previous calls may have crashed or failed to produce correct answer.

2010/10/02 - fot defineellipse3d.m, change initial visualization state

2010/10/02 - for fitgaussian3d.m, new default initial seed. more liberal tolerance. explicitly guard against nans.

2010/10/02 - in defineellipse3d.m, the fitted Gaussian no longer has a dc fixed to 0 but has an exponent now.

2010/09/27 - zerodiv.m no longer issues warnings when not <wantcaution>

2010/08/25 - explicitly put /home/knk in queuedaemon. this should be revisited eventually...

2010/08/25 - for outputfcnplot, we revamped this function [hack out ratio check; hack out <restol>; hack out NaN case for <numiters>]

2010/08/11 - queuedaemon, runme have been revamped and are not backwards-compatible.

2010/06/22 - unix_wrapper.m now reports status and result to the command window.

2010/06/15 - start using calccod.m instead of calccorrelation.m where appropriate (see subspaceapprox, fitprf, fitprfmulti, fitgabor2d, fitorientedgaussian2d, fitrbf2d)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SUMMARY OF FUNCTIONS

Here is a short summary of each function so that you can do a simple text search to see if there is a function that already does what you need.

matrix/

addvectors - add vectors of unequal sizes

blob - sum over successive groups along a certain dimension of a matrix

catcell - concatenate elements of a cell matrix

catmatrix - concatenate matrices (possibly unequal in size)

cellfunfirst - apply function to first element of a cell matrix (or the matrix itself)

cropvalidvolume - extract a subvolume of a matrix based on valid values

equalizematrixdimensions - make two matrices the same dimensions by expanding

fillout - repeat a matrix to fill a desired size

filterout - remove elements of a matrix according to a simple boolean operation

flatten - make into a row vector

fillmatrix - take a vector and fill a matrix with it

flipdims - flip some dimensions of a matrix

insertelt - insert element(s) in a vector

placematrix - place a 2D matrix inside another 2D matrix at an arbitrary position

placematrix2 - place a matrix inside another matrix

placematrixmulti - repeatedly randomly place a 2D matrix inside another 2D matrix

reshape2D - get into 2D for convenient manipulation

reshape2D_undo - undo what reshape2D does

reshapesquare - reshape a vector into a square matrix

rotatematrix - 2D rotation for an arbitrary matrix

sizefull - get size of a matrix for a certain number of dimensions

splitmatrix - take slices of a matrix and put them into a cell vector

splitruns - find runs of non-NaN numbers in a vector

squeezedim - remove a specific dimension that has only one element

squish - squish together the first n dimensions of a matrix

upsamplematrix - change the dimensionality of a matrix by upsampling

vflatten - make into a column vector

indexing/

calcposition - calculate the position of elements relative to a list

chunking - split a vector into chunks

firstel - return first element of a matrix

firstelc - return first element of a cell matrix

indexall - return an indexing helper for cell vectors

lastel - return last element of a matrix

linspacecircular - get equally spaced points in a circular domain

linspacefixeddiff - get equally spaced points given a fixed difference

linspacepixels - get equally spaced points that can be treated as centers of pixels

matrixindex - return different slices through a matrix based on an indexing matrix

permutedim - shuffle a matrix along a certain dimension or globally

picksubset - return a random subset of the elements in a matrix

removerepeats - get rid of runs of consecutive items

resamplingindices - get indices corresponding to the process of resampling

slicematrix - return a slice from a matrix

subscript - get elements using a vector or cell vector of indices

vectorsplit - split a vector into chunks

programming/

allocatememory - force allocation of a certain amount of memory (to induce swapping)

alwaysone - always return 1

alwayszero - always return 0

assignseparatevars - split a matrix and assign it to multiple variables

assigntobaseworkspace - assign all variables to the base workspace

checkmemoryworkspace - figure how much memory is being used in the caller's workspace

checkpathconflicts - check for .m file conflicts

choose - functional form of if-else

copymatrix - make a copy of a matrix with a subscript assignment on-the-fly

consolidatemat - consolidate results from multiple .mat files into a single .mat file

consolidatematdir - consolidate results from .mat files in a directory

decodenum - undo encodenum.m

defaultoptimset - return a default optimset options structure

encapsulate - evaluate a function at multiple values and encapsulate results into a cell vector

encodenum - encode a number as a string of uppercase letters

enforcenan - set cases with all 0 to NaN

evalme - evaluate multi-line input in the MATLAB workspace

gethostname - get the hostname

getpid - get the process ID for this instance of MATLAB

gettimestring - return the current date/time as a simple integer string

GPUconv - convert to GPU format

GPUok - return whether we should try to use the GPU

gunziptemp - gunzip a file on the fly

identity - return an argument unchanged

infiniteloop - do nothing forever

inputmulti - take multi-line string input from stdin

isfinitenum - evaluate whether each element is finite and numeric

isint - evaluate whether each element is an integer

isrowvector - evaluate whether matrix is 1 x n (where n >= 0)

maketempdir - make a new empty temporary directory and return the path to it.

mergestructs - merge one struct into another

mkdirquiet - make a directory, suppressing warnings

mtimesmulti - multiply arguments together

passmulti - pass multiple arguments to a function from a cell vector

pause2 - pause but also return an output

playalarm - play an alarm to get the user's attention

plusmulti - add arguments together

processchunks - perform an operation on successive chunks of a big matrix to save on memory usage

promptforfile - get a .mat file name from the user

repeatuntil - call a function until a condition is satisfied

reportmemoryandtime - use a warning to report the current memory usage and the current time

rmdirquiet - remove a file or directory, suppressing warnings

rowfun - apply a function to each row of a 2D matrix

runmatlabinbg.pl - run MATLAB in the background for a single function/script call

sanitycheck - print out some fprintf statements about values in a matrix

saveemptymat - save an empty .mat file

setrandstate - induce randomness by (randomly) setting the seed of rand and randn

sgerun2 - run MATLAB code using the Sun Grid Engine (SGE)

statusdots - write out dots (.) indicating progress of code execution

subsetfun - apply a function to successive subsets of a vector

swap - swap two arguments

unix_wrapper - a nice wrapper for unix.m

string/

cell2str - convert 2D cell matrix into string representation

cell2str2 - convert cell vector of strings into a single string that names each string

fixstr - fix string for use with MATLAB's figure functions

makedirid - return a string with elements of a path joined with '_'

makeletters - generate a cell vector of letter characters

mat2cellstr - convert a matrix of numbers into a cell matrix of strings

matchword - return the first word found in a string

randomword - generate a random word consisting of capital letters

sortnumerical - sort a cell vector of strings according to trailing integers

strsplitalt - split a string based on a pattern

io/

absolutepath - return the absolute path to a given file

clearexcept - clear all variables except certain variables

getextension - get the extension (e.g. '.txt') of a filename

loadbinary - load numbers from a binary file

loadexcept - load variables from a .mat file, excluding certain variables

loadmaybe - load variable from a .mat file, but failing gracefully

loadmulti - concatenate or merge a single variable from multiple .mat files

loadmulti2 - load multiple variables from one .mat file

loadtext - load strings from a text file

matchfiles - return strings containing paths to matched files and/or directories

multifile - apply a function to multiple files

niiload - load specific voxels from NIFTI files containing 4D data

raw2dload - load specific columns from binary files containing 2D data

savebinary - save numbers to a binary file

saveexcept - save all variables to a .mat file, excluding certain variables

savetext - save strings to a text file

shuffletext - shuffle lines in a text file

stripext - remove the extension from a file name

stripfile - remove the file name from a string

math/

addnoise - add some noise to a matrix

allzero - check whether all elements are equal to zero within some tolerance

ang2complex - convert angles to unit-magnitude complex numbers

chunkfun - apply a function to successive chunks of a vector

chunknormalize - subtract mean of successive chunks of a matrix

calccod - calculate coefficient of determination (R^2)

calccodcell - calccod for cell vectors of matrices

calccorrelation - calculate Pearson's correlation coefficient (r)

calcmdse - calculate the median and the standard error on the median

calcmdsepct - calculate the median and percentiles on bootstraps of the median

calcsparseness - calculate sparseness

calczscore - convert to z-scores

circularavg - average numbers, respecting circularity

circulardiff - difference between two values defined in a circular domain

circularshiftandsum - take a vector, circularly shift it multiple times, and sum

clipoutliers - clip the outliers of a matrix

constructpathonsphere - connect points on the unit sphere

countinstances - count how many 1s, 2s, etc. are in a matrix

divnorm - apply divisive normalization to a matrix

matchgain - figure out scalar factor to match one set of data to another

meanandse - calculate the mean and standard error

meancell - take the mean for data that are split into cell matrices

mod2 - like mod.m but return 0 outputs as the modulus itself

mod4 - like mod.m but restrict outputs to the range [-modulus/2,modulus/2]

mtimescell - do matrix multiplication but with an argument split into a cell vector

nanreplace - replace NaNs with a specified value

nanreplace2 - replace NaNs with a specified value (alternative mode of operation)

nantoclosest - replace NaNs with the nearest valid values

negrect - negative-rectify

negreplace - replace negative values with a specified value

normalizerange - scale to fit within a specific range

normalizemax - scale such that max value is 1

posnegrect - positive- and negative-rectify

posrect - positive-rectify

restrictrange - truncate values to fit within a range

robustrange - calculate a robust range of a set of values

signedarraypower - take the array power but preserve sign

signforce - return +1 for positive or zero elements; -1 for negative elements

stdquartile - return something like std but in the percentile sense

unitlength - normalize to have unit length (L2-norm is 1)

unitlengthfast - normalize to have unit length (L2-norm is 1)

l1unitlength - normalize to have unit length (L1-norm is 1)

vectorlength - calculate vector length (L2-norm)

l1vectorlength - calculate vector length (L1-norm)

zerodiv - divide but with special handling for division by zero

zeromean - subtract off the mean

stats/

applyfiltermultidim - apply filters for the case of images with multiple features

bootstrap - apply a function to bootstrap samples drawn from a vector (useful for computing standard error)

bootstrapdim - more general version of bootstrap

calcconfusionmatrix - calculate a confusion matrix (i.e. covariance, cross-product, etc.)

calcentropy - calculate entropy based on a matrix with counts

calcggaussianlikelihood - calculate likelihood of a set of points assuming independent generalized Gaussian distributions

calcintrinsicdim - calculate number of eigenvectors needed to achieve a certain amount of the variance in a matrix

calcmutualinformation - calculate mutual information between two matrices

calcmutualinformationcontinuous - calculate mutual information between two matrices in a continuous way

calcmvgaussianpdf - calculate multivarate Gaussian probability density function

calcnoiseceiling - calculate how well a set of data can be predicted, taking into account the intrinsic noisiness of the data

calcoptimalhistbins - calculate the optimum number of bins to use for hist.m

calcrbflikelihood - calculate likelihood of a set of points given a collection of RBFs

calcrectlikelihood - calculate likelihood of a set of points given a collection of directions (half-squared responses)

calcrobustsummary - calculate the median and one-half of the central 68% range

calcshrunkencovariance - use shrinkage and cross-validation to obtain more robust estimates of covariance

calcsurfaceareanball - calculate surface area of a unit n-ball

centerofmass - calculate the center-of-mass of a matrix

constructdctmatrix - construct a matrix with DCT-II basis functions in the columns

constructdftmatrix - construct a matrix with DFT basis functions in the columns

constructfiltersubsample - construct 2D filters according to a subsampling scheme

constructfiltertiling - construct filters by tiling a single 2D filter

constructnearestpsdcovariance - find the nearest positive semidefinite matrix

constructpolynomialmatrix - construct a matrix with polynomials in the columns

constructpolynomialmatrix2d - evaluate polynomial basis functions defined in 2D at some locations

constructpolynomialmatrix3d - evaluate polynomial basis functions defined in 3D at some locations

convertcovariancetocorrelation - convert a covariance matrix to a correlation matrix

evaldivnorm - evaluate divisive-normalization function at some values

evalgaussian1d - evaluate 1D Gaussian function at some coordinates

evalgaussian2d - evaluate 2D Gaussian function at some coordinates

evalgaussian2doriented - evaluate 2D Gaussian function (that can be rotated) at some coordinates

evalgaussian3d - evaluate 3D Gaussian function at some coordinates

evalgeneralizedgaussian - evaluate generalized Gaussian pdf

filter2subsample - apply filter2 and then subsample the result

findlocal - find points that are close to a given point

findtailthreshold - determine a threshold for a distribution of data using a GMM with 2 Gaussians

fit2dpolynomialmodel - use polynomial basis functions to fit a surface defined in 2D, allowing scale factor for different cases

fit3dpolynomialmodel - use polynomial basis functions to fit a surface defined in 3D, allowing scale factor for different cases

fit3dpolynomialmodel2 - use polynomial basis functions to fit a surface defined in 3D, allowing DC offset for different cases

fitdivnorm - fit divisive-normalization function

fitgaussian1d - fit 1D Gaussian function

fitgaussian2d - fit 2D Gaussian function

fitgaussian2doriented - fit 2D Gaussian function that can be rotated

fitgaussian3d - fit 3D Gaussian function

fitl1line - perform linear regression but use an L1-error metric

fitline2derror - fit a line to a set of 2D points using an error metric that is sensitive to both x and y

fitnonlinearmodel - a useful wrapper around MATLAB's lsqcurvefit.m function

fitnonlinearmodel_consolidate - consolidate .mat files written by fitnonlinearmodel

fitnonlinearmodel_helper - a helper function for fitnonlinearmodel.m

fitrbfpdf - fit a simplified mixture-of-Gaussians probability density function model using k-means

fitrectpdf - fit a rectified squared model using k-means and interpret as a PDF

fitrectdensity - fit a rectified squared model using k-means and interpret more like ANN

gradientdescent - perform gradient descent or forward stagewise regression

gradientdescent_wrapper - perform n-fold averaging technique for gradientdescent.m

localregression - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on one dimension)

localregression2d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on two dimensions)

localregression3d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on three dimensions)

localregression4d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on four dimensions)

localregressionbandwidth - cross-validate to determine the optimal bandwidth for local regression

olscontrol - perform ordinary least-squares regression while controlling for some given regressors

olsmatrix - perform ordinary least-squares regression

olsmatrix2 - perform ordinary least-squares regression (fast mode)

outputfcnplot - plot parameter history during an optimization

outputfcnsanitycheck - explicit check on the size of the residuals to prevent infinite computation

performfreqwhitening - flatten the average amplitude spectra of a set of images

performpcawhitening - whiten a matrix in the PCA sense

projectionmatrix - project out a linear subspace using ordinary least-squares regression

randgg - generate random numbers from a generalized Gaussian

randintrange,randintrange2 - randomly choose integers within a given range

randnmulti - generate random numbers from a multivariate Gaussian

randomization - calculate p-values using randomization

randomorthogonalbasis - generate a random set of orthogonal basis functions

resamplingtransform - a utility function to deal with cross-validation ordering as used in fitnonlinearmodel.m

roundpvalue - round p-value up to have the form Xe-Y

runkmeans - run the k-means clustering algorithm

subspaceapprox - calculate correlation between a subspace and a vector

timeseries/

calcpeak - calculate the peak of some time-series data (using interpolation)

constructbutterfilter1D - construct a Fourier-domain Butterworth filter

conv2run - convolve but keep runs separate

deconvolvevectors - deconvolve one vector from another vector

fouriertospace1D - convert magnitude filter in Fourier domain to the space domain

generatepinknoise1D - generate samples of pink noise

processmulti1D - apply a function that expects a single vector to multiple vectors

sincshift - shift time-series data using sinc interpolation and padding

tseriesinterp - interpolate time-series to achieve a new sampling rate

tsfilter - filter time-series data with a Fourier-defined magnitude-based filter

imageprocessing/

applymultiscalegaborfilters - filter images with a set of multi-scale Gabor filters

applymultiscalegaussianfilters - filter images with a set of multi-scale Gaussian or Difference-of-Gaussians filters

ba_interp3_wrapper - convenient wrapper for the 3D interpolation toolbox ba_interp3

calcamplitudespectrum - calculate a smooth function relating spatial frequency to amplitude

calccpfov - return number of cycles per FOV associated with fft2 after fftshifting

calccpfov1D - return number of cycles per FOV associated with fft after fftshifting

calccpfov3D - return number of cycles per FOV associated with fftn (in three dimensions) after fftshifting

calcimagecoordinates - return coordinates of the pixels of an image

calcpositiondifferentfov - determine the coordinates of a new image with respect to an original image

calcunitcoordinates - return coordinates of points equally spaced within the square bounded by -.5 and .5

checkimagesize - inspect pixel dimensions of a batch of image files

chtoim - reshape image(s) from images x res*res to res x res x images

concatimages - concatenate multiple images together

constructbutterfilter - construct a Fourier-domain Butterworth filter (for images)

constructbutterfilter3D - construct a Fourier-domain Butterworth filter (for volumes)

constructcosinefilter - construct a Fourier-domain cosine-tapered filter

constructorientationfilter - construct a Fourier-domain orientation filter (von Mises distribution)

constructsmoothingfilter - construct a space-domain 2D or 3D Gaussian filter

constructwhiteningfilter - construct a Fourier-domain whitening filter

detectedges - detect edges in an image using simple scheme

evaldog2d - evaluate 2D Difference-of-Gaussians function at some coordinates

evalgabor2d - evaluate 2D Gabor function at some coordinates

evalgrating2d - evaluate 2D sinusoidal grating function at some coordinates

evalorientedgaussian2d - evaluate oriented 2D Gaussian at some coordinates

evalrbf2d - evaluate 2D radial basis function at some coordinates

extractwindow - easily pull out different chunks of an image

fitgabor2d - fit 2D Gabor function

fitorientedgaussian2d - fit oriented 2D Gaussian

fitrbf2d - fit 2D radial basis function

fftshift2 - apply fftshift along the first two dimensions

flattenspectra - apply spatial frequency filtering to flatten the spectra of some images

fouriertospace - convert magnitude filter in Fourier domain to the space domain

gabortransform - perform Gabor transformation on one or more images

generatepinknoise - generate samples of pink noise

generaterandomphase - generate random phases suitable for multiplication with output of fft2

generatewinnermap - compress multidimensional data by using hue and brightness to represent the maximum value along a dimension

getsamplebrain - return a brain volume

getsampleimage - return a 500x500 grayscale natural image

ifftshift2 - apply ifftshift along the first two dimensions

imagefilter - filter images with a Fourier-defined magnitude-based filter

imagefilter3D - filter volumes with a Fourier-defined magnitude-based filter

imagesearch - search through image space to minimize some cost function

imagesequenceconcatenate - concatenate multiple image files together

imagesequencetomovie - make a QT movie from images

imaveragefiles - average multiple image files together

imcropfiles - manually define a crop region and then apply to one or more image files

imreadmulti - load in multiple images

imrectsquare - enforce square and integer crop to an imrect

imrectimagecrop - return a valid image crop from imrect

imresizedifferentfov - resize an image but use a different field-of-view

imresizememory - call imresize on a bunch of images, minimizing memory usage

imwritemulti - write multiple images to multiple files

imtoch - reshape image(s) from res x res x images to images x res*res

makecircleimage - draw a circle as an image

makecolorimagestack - convert a 4D matrix containing multiple color images into a 3D matrix

makeconcentricgrating2d - make a concentric 2D sinusoidal grating

makedog2d - make a 2D Difference-of-Gaussians

makegabor2d - make a 2D Gabor

makegaussian2d - make a 2D Gaussian

makegaussian3d - make a 3D Gaussian

makegrating2d - make a 2D sinusoidal grating

makegratings2d - make a set of 2D sinusoidal gratings

makeimagestack - convert a 3D matrix containing multiple images into a 2D matrix

makeimagestack_wrapper - run makeimagestack for multiple 3D matrices

makeimagestack3dfiles - like makeimagestack but write out some convenient .png files

makeorientedgaussian2d - make an oriented 2D Gaussian

makesquareimage - draw a square as an image

maskmultiscalegaborfilters - modify results of applymultiscalegaborfilters according to a binary mask

phasescrambleimage - blend image with random-phase image

placeimageintosquare - place an image anywhere within another image

processimages - perform some function on many image files

processmulti - apply a function that expects a single image to multiple images

scrambleimage - scramble an image, preserving chunks of a certain size

smoothvolumes - use a Gaussian filter to smooth one or more 3D volumes

socmodel - compute the response of the SOC model to some stimuli

splitimages - split images into chunks

unitlengthfft2 - unit-length-normalize a Fourier domain filter

varycontrast - vary the contrast of an image

viewimage - do some visualizations for a given image

viewimages - visualize many images at once

viewmovie - view a series of images as a movie (or write a series of image files)

visualizemultiscalegaborfilters- visualize points associated with applymultiscalegaborfilters

figure/

addlogticks - add logarithmic ticks to a figure whose data have already been log-transformed

axissquarify - make axis equal-aspect, square, and origin-centered and draw unity line

errorbar2 - draw error bars (as lines)

errorbar3 - draw error bars (as a polygon)

figureprep - make an invisible figure window

figurewrite - write the invisible figure window to an image file

getcolorchar - take an integer and get a color character

getfigurepos - return figure position (in normalized units)

hist1dimage - draw a histogram as a vertical 1D image

histrobust - run hist but ensuring a robust range

imageactual - draw an image at its native resolution

imagescmulti - make separate figure windows for multiple images

plotorientedbar - plot an oriented bar

plotrectangle - plot a rectangle

printnice - print figure window to file

setaxispos - set axis position (without mangling the Units setting)

setfigurepos - set figure position (without mangling the Units setting)

scatterb - do a binned scatterplot

scatterline - use local linear regression to summarize a scatterplot

scattersparse - do a scatterplot but limit the number of points

scatterimagesparse - do a image scatterplot and limit the number of points

squarify - figure out a roughly evenly balanced number of rows and columns necessary to fit a certain number of elements

straightline - draw horizontal or vertical lines

subplotresize - make the subplots of a figure as big as possible

colormap/

cmapang - hue-based colormap suitable for circular ranges (e.g. angles)

cmapangLR - like cmapang.m but left-right flipped

cmapangLVF - like cmapang.m but focused on the left visual field

cmapangRVF - like cmapang.m but focused on the right visual field

cmapdistinct - hue-based colormap for cases where you want maximally distinct colors

cmaplookup - take values and get colors from colormap

cmaphue - hue-based colormap suitable for circular ranges

cmapsinglecolor - generate colormap that mixes from one color to a second color

cmapsign - blue-black-red colormap suitable for ranges like [-X X]

cmapsign2 - blue-white-red colormap suitable for ranges like [-X X]

cmapsign3 - blue-lightgray-red colormap suitable for ranges like [-X X]

cmapsign4 - cyan-blue-black-red-yellow colormap suitable for ranges like [-X X]

cmaptab10 - a set of 10 discrete colors

cmapturbo - jet-like colormap

colorinterpolate - make a colormap by interpolating between key colors

drawcolorbar - draw a colorbar on the current figure

drawcolorbarcircular - draw a circular colorbar on the current figure

graphic/

calcdistpointline - calculate the distance between one or more points and a line

circlewithin - determine whether one or more circles are contained within a certain circle

coordangle - calculate coordinates of an angle

coordpolygon - calculate coordinates of an equilateral polygon

createrescalingmatrix - construct a transformation matrix that rescales with respect to (0.5,0.5,0.5)

defineellipse3d - allow user to define a 3D ellipse on a 3D volume

drawarrow - draw an arrow (in two dimensions)

drawbar - draw an oriented bar

drawbars - draw a set of oriented bars

drawbartexture - draw a random array of oriented bars

drawcheckerboard - draw an oriented checkerboard

drawcheckerboards - draw a set of oriented checkerboards

drawclosedcontour - draw a generic closed contour shape

drawclosedcontours - render several closed contours

drawdartboard - draw a radial checkerboard (dartboard)

drawellipse - draw a complete or partial ellipse (includes circles and arcs as special cases)

drawmultiscale - place objects at multiple scales on a pink-noise background

drawpolargrid - draw a polar grid consisting of rings and spokes

drawrectangle - draw a rectangle

drawsector - draw a sector

drawtext - draw a word

drawtexts - render several words

renderfigure - render the current figure into an image (assumed to be square)

xyzscale - construct a scaling transformation matrix

xyztranslate - construct a translating transformation matrix

xyzrotate_* - construct a rotation transformation matrix

xyzrotatetoz - return rotation transformation matrix to align a vector with positive z-axis

mri/

calchrfpeak - estimate the peak (positive or negative) value of an HRF

changevolumeres - change the resolution of a volume while preserving field-of-view

computebrickandindices - determine a brick into a 3D binary volume

computetemporalsnr - compute the stability of a series of 3D volumes over time

condition_split - perform condition-splitting on a set of design matrices

constructhrfmodeldct - return a matrix of DCT-II basis functions for modeling HRFs

constructhrfmodeldelta - return a matrix of delta basis functions for modeling HRFs

constructhrfmodelspline - return an spline-based HRF model

constructstimulusmatrices - construct design matrix for a finite impulse response (FIR) model

copyxform_nii - propagate transformation-related fields from one NII file to others

coregistervolumes - coregister one volume to another

createspmmatrix - return the default SPM transformation matrix

dicomloaddir - load volumes and voxel-size information from a DICOM directory

evaldoublegamma - evaluate double-gamma function at some x-values

expdesignefficiency - calculate efficiency of an experimental design

fithrfgammadouble.m - fit a double-gamma function

fmriquality - write figures to inspect the spatial quality of fMRI volumes

fstoint - go from FreeSurfer space to our internal space

getcanonicalhrf - return a canonical HRF (based on empirical data) for arbitrary duration and TR

getcanonicalhrf2 - return canonical Early and Late HRFs (based on empirical data) for arbitrary duration and TR

getcanonicalhrflibrary - return a set of canonical HRFs (based on empirical data) for arbitrary duration and TR

getsamplehrf - return some sample HRFs estimated from actual fMRI data

homogenizevolumes - homogenize a set of 3D volumes by dividing by fitted 3D polynomials

hrfgammadouble.m - evaluate a double-gamma function

inttofs - go from our internal space to FreeSurfer space

motioncorrectvolumes - perform motion correction for some volumes

preconditionvolume - precondition a 3D volume by clipping outliers and removing low-frequency signal variations

quantifymotionparameters - compute an intuitive summary metric of rigid-body motion during a run

resliceniftitomatch - use NIFTI header information to match one volume to another

settr_nii - set the TR in the header information of an NII structure

surfaceslice2 - figure out information relating voxels to vertices

undistortvolumes - resample volumes in order to correct for motion and distortion

write3dstack - write out extracted slices in three orientations from a 3D matrix

writespmfiles - write a series of volumes to individual SPM/ANALYZE files

pt/

calcfixationdotchangeperformance - perform analysis of behavioral data for experiments involving dot change detection

preparedigits - generate some digits and letters as uint8 images

pteyelinkoff - some eye-tracking related setup

pteyelinkon - some eye-tracking related setup

pton - initialize PsychToolbox stuff

ptoff - uninitialize PsychToolbox stuff

ptviewimage - show one or more images and allow user to position the images

ptviewmovie - show a stimulus movie

ptviewmoviecheck - check the results of ptviewmovie.m

runretinotopy - script for retinotopy experiment

showmulticlass - helper function for various experiments

external/ [code obtained from elsewhere]

hist2d.m - count histogram frequencies in two dimensions

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