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NeuroElf - all functions (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 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 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 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 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 fisherr2z - convert Pearson correlation into z values fitrobustbisquare - faster fitting function for robust bisquare fitrobustbisquare_img - faster fitting function for robust bisquare flexinterp - flexible data interpolation (up to 4D) flexinterpn_demo - demonstration of flexinterpn flexinterpn_method - call flexinterpn with one of the typical methods flexmask - flexible data masking 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 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 isinfnan - checking whether (any) element(s) are inf/nan isrealvarname - true for valid variable name isscalarcell - returns a boolean array with isscalar over cells 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 kendtau - returns the Kendall tau statistic for two vectors kendtaupairsign - return kendall tau ties-correction value 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 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 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 mesh_trianglestoneighbors - get mesh neighbors list from triangles mesh_trimapmesh - get triangular mapping for two spherical meshes minarray - minimize array size minmaxbbox - get minimum, maximum bounding box of objects minmaxmean - get min, max, and mean of data array (fast) 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 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 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 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 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 svmpredict - train libSVM based classifier svmtrain - train libSVM based classifier 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 threshmapc - thresholding a double map to 0…1 transmul - return the multiplication of M' * M u8str2double - convert numeric text (of multi-value data) to double 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 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 xffsrfwriteneighbors - write neighbors to SRF file 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

neuroelf_-_all_functions.1277180305.txt.gz · Last modified: 2010/06/22 06:18 by jochen