NeuroElf wiki

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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 - extended uses|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 1x1 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 1x4 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 4x4 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 =====