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neuroelf_-_all_functions

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NeuroElf - all functions

Toolbox base folder, M-file list only

  • 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
  • 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
  • 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)
  • 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
  • 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
  • dilate3d - perform 3D dilation with operator
  • dispslice - displays a 2-D dataset as an image
  • dispslicemovie - display slice movie
  • emptysrf - create an empty surface container
  • erode - 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)
  • 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
  • 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
  • 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
  • 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
  • importbesa - import EEG/MEG data from a set of BESA files
  • importfif - import FIF file
  • importvtcfromanalyze - import an FMR from Analzye files
  • importrfxglmfromspms - import SPM beta maps to a BrainVoyager GLM file
  • importvtcfromanalyze - 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(…)
  • isabsolute - returns true if the given path is absolute
  • 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
  • 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)
  • madist - 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_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
  • 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
  • multi_voi_avg - generate Multi-VOI averaging plots (abandoned for now)
  • 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_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
  • newnatresvmp - create natural resolution VMP object
  • noinfnan - replace Inf/NaN's in input with replacement value
  • 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
  • parsenumtable - parse a numeric table (deprecated, use u8str2double instead)
  • 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
  • pmfilter - 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
  • primes_b - generate list of prime numbers (abandoned for now)
  • 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)
  • 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
  • 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)
  • 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
  • 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)
  • 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
  • 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

Toolbox base folder, C-based functions

  • clustercoordsc.c
  • conv3d.c
  • cov_nd.c
  • findfirst.c
  • flexinterpn.c
  • flexmask.c
  • floodfill3c.c
  • gluetostringc.c
  • isemptycell.c
  • isinfnan.c
  • isscalarcell.c
  • joinlayers.c
  • kendtaupairsign.c
  • limitrangec.c
  • medianc.c
  • mesh_morph.c
  • mesh_trianglestoneighbors.c
  • mesh_trimapmesh.c
  • minmaxmean.c
  • normcdfc.c
  • num2strtab.c
  • qsort.c
  • renderlayers.c
  • splittocellc.c
  • svdc.c
  • svmpredictc.c
  • svmtrainc.c
  • threshlutc.c
  • threshmapc.c
  • transmul.c
  • u8str2double.c
  • varc.c
  • xffsrfparseneighborsc.c
  • xffsrfwriteneighborsc.c

transimg functions

transio functions

xff functions

xff private functions (methods)

xfigure functions

xini functions

xprogress functions

neuroelf_-_all_functions.1277182747.txt.gz · Last modified: 2010/06/22 06:59 by jochen