NeuroElf - all functions

This page can be seen as a whole-sale reference to all function (M-) files of the toolbox. Currently, the documentation is spotty at best…

• BVQXfile - legacy function for BVQXtools users (passes to xff)
• ac2vmp - convert activation_clusters MAT file (Tor Wager tools) to VMP
• acpc2tal - convert AC-PC coordinates into TAL coordinates
• acsvread - reads a text based (non-numeric) csv file
• afni_parse - internal parser for AFNI HEADer file structures
• alphasim - simulate noise data to estimate cluster threshold
• analyze_setendian - set endian type for Analyze files
• analyzetype - return properties of analyze image datatype
• any2ascii - packs simple as well as complex variables into ascii
• applybvtrf - apply BV transformation matrix to system coords
• applyfdr - apply FDR thresholding to given statistic
• applyspmsnc - apply SPM's spatial normalization (*_sn.mat) to coordinates
• asciiread - reads a textfile into one char array
• asciitab - create custom ASCII representation of 2-D matrix
• asciiwrite - writes a textfile from a char array to file
• auroc - compute area under ROC
• autocorr - estimate auto-correlation in data
• averagepmps - average PMP objects and create new object (abandoned for now)
• averagevmrs - average VMRs
• barycoord - returns barycentric coordinates of point vs. triangle
• bcc2area - lookup TalairachBrain.vmr color codes
• binread - reads a binary into one uint8 array
• binwrite - writes a binary stream from a char/uint8 array to file
• bitdump - dump bits in a uint buffer (abandoned for now)
• bstrapbca - bootstrap statistic using BCa
• bstrappct - bootstrap statistic using percentile
• bvcoordconv - converting coordinates for BV
• bvtrf - compile a transformation matrix as in the 3D volume tools
• bvxaddvartofile - add a variable to an existing BVX file (abandoned for now)
• bvxcreatefile - create new BVX file (abandoned for now)
• calcbetas - perform GLM regression
• cellipse - confidence ellipse coordinates for scatter plot
• checkstruct - check an 1×1 struct for validity
• checksyntax - checks a snippet of code for syntax validity
• clearxffobjects - issue ClearObject call on several objects
• clustercoords - get list of clusters in volume
• clustercoordsc - get list of clusters in volume (MEX file stub/help)
• clustermeshmap - cluster a SMP/SRF based map
• clustermeshmapbin - cluster binary mesh-based map
• clustervol - cluster volume with threshold
• clustervol_struct - create cluster struct (cell array) for TW tools
• colcode2uint32 - convert from colcode to uint32 array
• colorpicker - pick a color from the RGB/HSV color space
• computehrv - compute HRV from onsets
• conjval - conjugate value (same sign, min abs value with sign)
• conjvalp - conjugate pvalues (same sign, max value with sign)
• conv3d - perform 3D convolution (MEX file stub/help)
• convones - convoles a function with a number of consecutive ones
• correlinvtstat - convert t-statistic into correlation value
• correlpvalue - pvalue of correlation coefficient
• correltstat - convert correlation value into t-statistic
• corrmap - correlation map
• cov_nd - computes covariance and corrcoefs for vector pairs in N-D (MEX file stub/help)
• cpfile - copies a file (deprecated! use copyfile instead)
• crawford_abnorm - calculate Crawford's score abnormality measure (abandoned for now)
• crawford_diff - calculate Crawford's single case t-score (abandoned for now)
• crawford_diss - calculate Crawford's single case dissociation t-score (abandoned for now)
• createfmr - create a FMR from a set of IMA/DCM files
• createmarkervmp - create a VMP map with markers (electrode indicators)
• createsrf - create a SRF object from coordinates and triangles
• createvmr - create a VMR from a set of IMA/DCM files
• csvdbupdate - update the data field from CSV files
• custom_pwelch - compute Welch's periodogram power spectrum
• cutnpastemovie - create an AVI movie from bitmap files (abandoned for now)
• ddeblank - deblank on both ends of strings
• degclust - degree of clustering of data
• depcorrt - dependent correlation comparison t statistic
• detecthandles - detect handles in 3D segmentation (abandoned for now)
• detecthandles_o - detect handles in 3D segmentation (abandoned for now)
• dicom4todmr - cheap try to convert a DICOM4 file into DMR/DWI
• dicom4tofmr - cheap try to convert a DICOM4 file into FMR/STC
• dicom_dic - internally used DICOM dictionary function
• dilate3d - perform 3D dilation with operator
• dispslice - displays a 2-D dataset as an image
• dispslicemovie - display slice movie
• dividetrimesh - divide triangular mesh into smaller triangles
• emptysrf - create an empty surface container
• erode3d - perform 3D erosion with operator
• exceltocoords - converts MS-Excel notation into 1×4 double array
• extcaller - from where was a call issued
• fdr_thresholds - compute probability thresholds for q(FDR) levels
• fendian - return an argument suitable for fopen (endianess)
• fieldsize - get size of struct field(s) in bytes
• fileguessendian - guess endian type of (partial) file content
• filesize - return a file's size in bytes
• fileswapendian - swap endian type of (partial) file content
• findfiledir - find a named file or directory
• findfiles - Linux/UNIX-like find command/function
• findfirst - find first (or last) element != 0 in input (MEX file stub/help)
• fisherr2z - convert Pearson correlation into z values
• fitrobustbisquare - faster fitting function for robust bisquare
• fitrobustbisquare_img - faster fitting function for robust bisquare
• fitrobustbisquare_multi - faster fitting function for robust bisquare multiple models
• flexinterpn - flexible data interpolation (up to 4D) (MEX file stub/help)
• flexinterpn_demo - demonstration of flexinterpn
• flexinterpn_method - call flexinterpn with one of the typical methods
• flexmask - flexible data masking (MEX file stub/help)
• floodfill3 - keep adjacent values from seed point
• fmriqasheet - create figure with output of fmriquality
• fmriquality - get some quality assurance for fMRI data
• gammapdf - gamma distribution Probability Density Function (PDF)
• glmtstat - compute GLM t statistic
• gluetostring - glues a cell array of chars to one delimited char array
• gluetostringc - C-version of gluetostring (MEX file stub/help)
• gradsmooth - apply gradient based smoothing (abandoned for now)
• grep - GNU utils like grep
• gzip - console/shell interface for MATLAB (does NOT work on Windows!)
• hasfields - test whether a struct has the same fields as a template
• heartbeats - detect heart beats and frequency in physio data
• hexdump - dump hexadecimal values into string
• histcount - M-file for histcountc MEX function
• hrf - create canonical HRF shape
• hrfboost - assume that best fit is the (root of) sum of squares
• hxdouble - transform a double from/into a readable string
• hxsingle - transform a single from/into a readable string
• icbm2tal - apply non-linear normalization parameters from ICBM to TAL space
• icc - intraclass correlation calculation
• idftextread - read a text-converted IDF file (iView X)
• image_complexity - give image complexity estimate
• image_resize - resize a HxWxD numeric image to new measures
• image_rotate - rotate a HxWxD numeric image
• importbesa - import EEG/MEG data from a set of BESA files
• importfif - import FIF file
• importfmrfromanalyze - import an FMR from Analzye files
• importrfxglmfromspms - import SPM beta maps to a BrainVoyager GLM file
• importvmpfromspms - import several Analzye SPM map files
• importvmrfromanalyze - import a VMR from an Analzye file
• importvtcfromanalyze - import a VTC from Analzye files
• indepcorrz - independent correlation comparison z statistic
• initialalignment - perform the automatic IA
• invsystem - inverts the output argument order of system(…)
• isBVQXfile - legacy function for BVQXtools users (passes to isxff)
• isabsolute - returns true if the given path is absolute
• isectlp - compute intersection of line and plain (multi-dim)
• isemptycell - returns a boolean array with isempty over cells (MEX file stub/help)
• isinfnan - checking whether (any) element(s) are inf/nan (MEX file stub/help)
• isrealvarname - true for valid variable name
• isscalarcell - returns a boolean array with isscalar over cells (MEX file stub/help)
• istransio - check (and validate) object
• isxff - check (and validate) object
• isxfigure - perform validity check on input
• isxini - perform validity check on input
• jksample - Jack-Knife sampling indices
• joinlayers - joining of transimg layers into a HxWx3 image + alpha map (MEX file stub/help)
• kendtau - returns the Kendall tau statistic for two vectors
• kendtaupairsign - return kendall tau ties-correction value (MEX file stub/help)
• kendtaut - give approximate t-score for kendall tau (via monte-carlo)
• kendtauz - give approximate z-score for kendall tau (via formula)
• kurt - compute kurtosis of data
• limitrangec - limit data to a range (MEX file stub/help)
• limittorange - limit data to percentile range
• linscale - linear scaling transform
• lsqueeze - linear squeeze into Nx1 array
• ltriasc - ASCII form of a lower triangle matrix (for Mx)
• madistd - Mahalanobis distance of single data argument
• mainver - get matlab main version
• makelabel - returns a valid label from input
• mappvalue - convert stats to pvalue (signed)
• maxgrad - return maximum direct neighbor gradient (diff) per voxel
• maxpos - return not the max but only the pos (deprecated, use minmaxmean instead)
• meannoinfnan - build mean of elements other than Inf/NaN
• meanpsctrans - perform PSC transformation after regression
• medianc - picking the median of an array using quickselect (MEX file stub/help)
• memusage - give the current memory usage of the calling function
• mergehemivmrs - merge segmented VMRs of LH and RH
• mesh_morph - morph the coordinates of a mesh (MEX file stub/help)
• mesh_neighborsarray - create a CxN neighbors list (0-filled)
• mesh_reconstruct - create direct border reconstruction information
• mesh_trianglestoneighbors - get mesh neighbors list from triangles (MEX file stub/help)
• mesh_trimapmesh - get triangular mapping for two spherical meshes (MEX file stub/help)
• minarray - minimize array size
• minmaxbbox - get minimum, maximum bounding box of objects
• minmaxmean - get min, max, and mean of data array (fast) (MEX file stub/help)
• minpos - return not the min but only the pos (deprecated, use minmaxmean instead)
• mkadir - create an absolute directory (unlike to MATLAB's mkdir)
• mltype - return Matlab's datatype association
• mmregress - multi-model regression
• mni2tal - converts coordinates from MNI brain to best Talairach guess
• mpackage - MatLab Installation Package Generator
• mstrrep - replace multiple patterns (multi strrep)
• mtc_concat - concatenate MTCs
• mtimesnd - mtimes (AxB * BxC) over dims 3, 4, …
• multimatch - match two lists of strings and return matched in first
• multiset - set properties for multiple handles
• multislicetovol - convert a multislice MxNx1 image file to a XxYxZ 3-D volume
• ne_fastica - perform ICA with FastICA algorithm
• neuroelf_build - return the build number of NeuroElf
• neuroelf_file - return file contents
• neuroelf_gui - the NeuroElf graphical user interface (GUI)
• neuroelf_license - display NeuroElf license
• neuroelf_makefiles - create additional files used by NeuroElf
• neuroelf_makelibs - compile MEX functions (mex/compiler needed!)
• neuroelf_pack - create installation/update/diff package
• neuroelf_path - get path where NeuroElf is installed
• neuroelf_setup - NeuroElf post installation setup
• neuroelf_version - return the version of NeuroElf
• newhdr - create new HDR/NII object
• newhiresvmr - create new hi-res VMR
• newnatresvmp - create natural resolution VMP object
• noinfnan - replace Inf/NaN's in input with replacement value
• normcdfc - M-file stub for MEX file
• normvecs - normalize vector lengths to 1
• num2strtab - creates a tabular data output of a numeric data table (MEX file stub/help) NOT FUNCTIONAL YET
• orthimage - compute orthogonality matrix (for SPM like display)
• orthsdm - orthogonalize SDM object in file
• orthvec - cheap orthogonalization
• orthvecs - orthogonalize vectors against each other
• ostype - returns information about the currently used OS
• osz - returns ones(size(svzar))
• packmosaic - pack one dimension into one/two other(s)
• pairs - returns the pairs of values in a vector/matrix
• parseformula - parse a formula
• parseopts - parse optional input arguments with defaults
• partoanalyze75 - convert PAR/REC into Analyze 7.5
• pinvc - pseudo-inverse using svdc
• plotcurves - plot different curves and select those of interest
• pmbfilter - apply a poly-mask bias filter to an image
• pmpalignment - compute alignment PMPs (abandoned for now)
• poolgroups - pool several sample groups into one stats analysis
• prefilter - spike/shift/resonance filter data
• progresscount - display progress in console as a step based counter (abandoned for now)
• psctrans - perform PSC transformation on time course
• qsort - sorting of 1-D vectors (MEX file stub/help)
• rangegrid - expand 4xD range definition into coordinates (using ndgrid)
• ranktrans - return rank transform of data
• rbalign - rigid-body alignment of one volume to a volume stack
• readbesa - read in BESA export files for further processing
• readhrv - reads a heart rate variability text file (abandoned for now)
• readpar - read a Philips PAR file
• reccheck - check quality of REC file (using a subset of fmriquality)
• regress_coords - find best matching quaternion t to match coordinates
• relfilename - build relative filename from two given files
• renamedicom - rename a dicom file according to a pattern
• renamefields - renames fields in a struct
• renamefile - renames a file to another filename
• render_vol - 3-D rendering of an spm_vol struct (abandoned for now)
• renderlayers - rendering of transimg layers into a HxWx3 uint8 image (MEX file stub/help)
• replacerobmean - replace outliers with robust mean estimate
• resampleaa - anti-aliased resampling of data
• rmean - re-weighted mean
• robcorrcoef - robust correlation coefficient using bisquare weighting
• robscatter - scatter data with option of robustfit
• robustF - compute F scores given robust stats
• robustmean - robust mean estimation
• robustnsamplet - performs robust fit and computes t scores
• robustnsamplet_img - apply robust N-sample test to set of images
• robustt - compute t scores given robust stats
• samplefmrspace - samples a data slab at a given set of coordinates
• safecon - safe contrast computation taking missing values into account
• scaledata - automatically scale data between gray-scale boundaries
• scaleimage - automatically scale image data for image
• sdist - statistics distributions
• selectstruct - select from a struct with a clause (abandoned for now)
• setinfnantomean - set Inf/NaN in input to mean (over dim)
• setinfnantoval - set Inf/NaN in input to specific values(s)
• showspmrparams - display the rp_*.txt files of an SPM preprocessing
• showvtcsize - displays the sizes of VTCs found on the given path
• shrinkfg - shrink foreground where no changes to topology are made
• skew - compute skewness of data
• slydetrend - slyly detrends signal (abandoned for now)
• smoothdata3 - apply gaussian smoothing to 3D data
• smoothest3d - estimate smoothness map of residual time course data
• smoothkern - build N-dim smoothing kernel from FWHM
• smoothned - smooth non-equidistant data with a gaussian kernel
• smpdist - sample values from a discrete distribution
• solvesudoku - solve a sudoku puzzle
• spatent - spatial entropy of map values
• spherecoords - compute spherical coordinates
• spherecoordsinv - compute cartesian coordinates from spherical ones
• spheresrf - create a new sphere SRF
• spherevmr - create a 256x256x256 VMR for spherical region growing
• splitclustercoords - split coords of one cluster to subclusters
• splittocell - split a delimited string into a cell array
• splittocellc - C-version of splittocell (MEX file stub/help)
• spm5_preprojobs - create jobs and jobhelps from options
• spmitrf - uncompile an affine transformation into paramters
• spmmat2prt - convert a SPM.mat file into BV's PRT file(s)
• spmmat2sdm - convert a SPM.mat file into BV's SDM file(s)
• spmtrf - compile a transformation matrix as in spm
• srfalignment - align surface according to their folding patterns (abandoned for now)
• srfbvxalign - perform alignment of SRFs in a BVX file (abandoned for now)
• stcorrect - slice-time correction with additional options (NOT YET FUNCTIONAL)
• stoufferz - Stouffer's Z computation
• structdiff - compare two structures
• subclusters - separate mega cluster into sub-clusters
• subget - get a list of properties as a struct
• svdc - singular value decomposition (MEX file stub/help)
• svmpredict - train libSVM based classifier (MEX file stub/help)
• svmtrain - train libSVM based classifier (MEX file stub/help)
• tablesextract - create tables and extracts from GLM/VMPs
• tal2acpc - convert TAL coordinates into AC-PC coordinates
• tal2icbm - apply non-linear normalization from TAL to ICBM/MNI space
• tal2mni - converts coordinates from TAL brain to best MNI-space guess
• tcchecksum - checksum using textcrypt (not reliable for binary data) (abandoned for now)
• tcpdump_parse - parse tcpdump outfile (-w) file (abandoned for now)
• tcplot - plot timecourse data
• tdclient - send request to internet TDdatabase / local TD
• tdlabel - get NGM label of coordinate
• tdlocal2 - lookup local TD NiFTi image file for TalLabel
• tempfilter - filter temporal data
• textcrypt - en/decrypt a text message with a rotating key matrix
• textline - one line from a multi-line 1xN char array
• tfgparse - parses a xfigure TFG file into a struct
• tfmatrix - build 4×4 transformation matrix for different steps
• threshlutc - converting thresholded map to looked up colors (MEX file stub/help)
• threshmapc - thresholding a double map to 0…1 (MEX file stub/help)
• transmul - return the multiplication of M' * M (MEX file stub/help)
• u8str2double - convert numeric text (of multi-value data) to double (MEX file stub/help)
• uint322colcode - convert from uint32 to colcode array
• unpackmosaic - unpack mosaic from two dimensions into third
• unzerostring - removed string part after first (or last) zero
• utc - return utc-like time code (uint32)
• uunion - unsorted set union.
• varc - calculation of variance along dimension (MEX file stub/help)
• vmrspmcoreg - apply SPM's coregistration to two VMRs
• vmvreadpos - read one vertex movie position in a VMV file
• vmvwritepos - write one vertex movie position in a VMV file
• vtc_concat - concatenate VTCs
• winsorize - Winsorize data (to numbers of SD by numbers of passes)
• writestcfiles - create STC files from a 4D array (abandoned for now)
• xffcompare - compares two xff objects (or folders with files) (abandoned for now)
• xffsrfparseneighbors - parse neighbors from SRF file (MEX file stub/help)
• xffsrfwriteneighbors - write neighbors to SRF file (MEX file stub/help)
• xfigurecallback - make sure a callback has its own workspace
• zerodstring - fill a string with zero chars and fix length
• zsz - returns zeros(size(svzar))
• ztrans - perform z-transformation on time course

• applyspmsnc.c
• clustercoordsc.c
• conv3d.c
• cov_nd.c
• findfirst.c
• flexinterpn.c
• flexmask.c
• floodfill3c.c
• gluetostringc.c
• histcount.c
• hsvconv.c
• indexarray.c
• isemptycell.c
• isinfnan.c
• isscalarcell.c
• joinlayers.c
• kendtaupairsign.c
• limitrangec.c
• medianc.c
• mesh_morph.c
• mesh_neighborsarray.c
• mesh_reconstruct.c
• mesh_trianglestoneighbors.c
• mesh_trimapmesh.c
• minmaxmean.c
• normcdfc.c
• num2strtab.c
• pinvc.c
• qsort.c
• renderlayers.c
• splittocellc.c
• svdc.c
• svm2x.cpp
• svm3x.cpp
• svm3xmodel.c
• svmpredictc2x.c
• svmpredictc3x.c
• svmreadc3x.c
• svmtrainc2x.c
• svmtrainc3x.c
• svmwritec3x.c
• threshlutc.c
• threshmapc.c
• transmul.c
• u8str2double.c
• varc.c
• xffsrfparseneighborsc.c
• xffsrfwriteneighborsc.c

• @transimg/transimg - constructor
• @transimg/addlayer - add a layer to a transimg object
• @transimg/any2ascii - overload for any2ascii call
• @transimg/delete - delete (free) object
• @transimg/dellayer - remove layer(s) from transimg object
• @transimg/display - show object (rendered form)
• @transimg/handle - return internal handle
• @transimg/joinlayers - call joinlayers.MEX on layers of transimg object
• @transimg/render - render object
• @transimg/setbackground - set/alter background color
• @transimg/sethandle - set graphics handle
• @transimg/setlayer - replace layer with new data
• @transimg/setlayeralpha - replace alpha channel of layer with new data
• @transimg/setlayerpixel - replace pixel data of layer with new data
• @transimg/subsref - overload for subsref call

• @transio/transio - constructor
• @transio/any2ascii - overload for any2ascii call
• @transio/class - overload for class call
• @transio/datatype - return datatype of object
• @transio/display - overload for display call
• @transio/double - resolve data to double precision
• @transio/end - overload for end call
• @transio/filename - return filename of file storing underlying data
• @transio/isempty - overload for isempty call
• @transio/isinf - overload for isinf call
• @transio/isnan - overload for isnan call
• @transio/isnumeric - overload for isnumeric call
• @transio/littleendian - return little endian-ness (boolean value) of underlying data
• @transio/minus - overload for minus call
• @transio/mpower - overload for mpower call
• @transio/mrdivide - overload for mrdivide call
• @transio/mtimes - overload for mtimes call
• @transio/ndims - overload for ndims call
• @transio/numel - overload for numel call
• @transio/offset - return offset of data of object in underlying file
• @transio/plus - overload for plus call
• @transio/power - overload for power call
• @transio/rdivide - overload for rdivide call
• @transio/resolve - resolve data in native precision
• @transio/single - resolve data in single precision
• @transio/size - overload for size call
• @transio/subsasgn - overload for subsasgn call
• @transio/subsref - overload for subsref call
• @transio/times - overload for times call

• @xff/xff - constructor and settings
• @xff/Call - UI/workspace-safe way to call a method on an object
• @xff/any2ascii - overload for any2ascii call
• @xff/bless - remove garbage-collection stack-trace (persistence control)
• @xff/clear - free memory associated with an object
• @xff/delete - free memory associated with an object
• @xff/display - overload for display call
• @xff/eq - overload for eq call
• @xff/fieldnames - overload for fieldnames call
• @xff/get - overload for get call
• @xff/getcont - retrieve object's content as struct
• @xff/help - retrieve help on object
• @xff/methods - overload for methods call
• @xff/ndims - overload for ndims call
• @xff/ne - overload for ne call
• @xff/new - create new object (requires additional parameter)
• @xff/setcont - set object's content (field number and names must match!)
• @xff/size - overload for size call
• @xff/subsasgn - overload for subsasgn call
• @xff/subsref - overload for subsref call (also methods)

• @xff/private/bffdocu - documentation of BFF formats and functionality
• @xff/private/bffio - handle BFF (binary file formats) I/O
• @xff/private/bffparse - parse BFF specification files
• @xff/private/dcmio - handle DICOM I/O (input only)
• @xff/private/dicom_vr - DICOM value representations
• @xff/private/fifio - specifically handle FIF I/O (input only)
• @xff/private/tffdocu - documentation of TFF formats and functionality
• @xff/private/tffio - handle TFF (text file formats) I/O
• @xff/private/tffparse - parse TFF specification files
• @xff/private/xffclear - clear object (global variable memory)
• @xff/private/xffdetectmagic - detect filetype from magic tokens
• @xff/private/xffdtsfparsefibers - parse fibers in DTSF file
• @xff/private/xffdtsfwritefibers - write fibers to DTSF file
• @xff/private/xffformats - return parsed formats
• @xff/private/xffgetcont - get content of object
• @xff/private/xffgetscont - get super-structure content of object (incl. meta data)
• @xff/private/xffmethods - return available methods for object types
• @xff/private/xffrequestfile - file request dialog
• @xff/private/xffsetcont - set content of object
• @xff/private/xffsetscont - set super-structure content of object (update meta data)

• @xfigure/xfigure - constructor
• @xfigure/any2ascii - overload for any2ascii call
• @xfigure/display - overload for display call
• @xfigure/fieldnames - overload for fieldnames call
• @xfigure/methods - overload for methods call
• @xfigure/mlhandle - return Matlab graphics handle of xfigure object
• @xfigure/mstring - apply MultiString method to object
• @xfigure/subsasgn - overload for subsasgn call
• @xfigure/subsref - overload for subsref call

• @xini/xini - constructor
• @xini/display - overload for display call
• @xini/fieldnames - overload for fieldnames call
• @xini/methods - overload for methods call
• @xini/subsasgn - overload for subsasgn call
• @xini/subsref - overload for subsref call

• @xprogress/xprogress - constructor
• @xprogress/closebar - close xprogress bar and clear object
• @xprogress/subsasgn - overload for subsasgn call
• @xprogress/subsref - overload for subsref call