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neuroelf_-_all_functions [2010/06/22 04:19] – changed to list jochenneuroelf_-_all_functions [2011/03/31 00:03] – added new functions and completed list of methods jochen
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-====== NeuroElf - all functions (list only) ======+====== 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... 
 + 
 +===== Toolbox base folder, M-file list only ====== 
 +  * [[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   * [[acpc2tal]] - convert AC-PC coordinates into TAL coordinates
   * [[acsvread]] - reads a text based (non-numeric) csv file   * [[acsvread]] - reads a text based (non-numeric) csv file
-  * [[afni_parse]] - internal parser for AFNI HEADer file structures +  * afni_parse - internal parser for AFNI HEADer file structures 
-  * [[alphasim]] - simulate noise data to estimate cluster threshold+  * [[alphasim - extended uses|alphasim]] - simulate noise data to estimate cluster threshold
   * [[analyze_setendian]] - set endian type for Analyze files   * [[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    * [[any2ascii]] - packs simple as well as complex variables into ascii 
   * [[applybvtrf]] - apply BV transformation matrix to system coords   * [[applybvtrf]] - apply BV transformation matrix to system coords
   * [[applyfdr]] - apply FDR thresholding to given statistic   * [[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   * [[asciiread]] - reads a textfile into one char array
   * [[asciitab]] - create custom ASCII representation of 2-D matrix   * [[asciitab]] - create custom ASCII representation of 2-D matrix
   * [[asciiwrite]] - writes a textfile from a char array to file   * [[asciiwrite]] - writes a textfile from a char array to file
 +  * [[auroc]] - compute area under ROC
   * [[autocorr]] - estimate auto-correlation in data   * [[autocorr]] - estimate auto-correlation in data
   * averagepmps - average PMP objects and create new object (//abandoned for now//)   * averagepmps - average PMP objects and create new object (//abandoned for now//)
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   * [[binwrite]] - writes a binary stream from a char/uint8 array to file   * [[binwrite]] - writes a binary stream from a char/uint8 array to file
   * bitdump - dump bits in a uint buffer (//abandoned for now//)   * 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   * [[bvcoordconv]] - converting coordinates for BV
   * [[bvtrf]] - compile a transformation matrix as in the 3D volume tools   * [[bvtrf]] - compile a transformation matrix as in the 3D volume tools
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   * bvxcreatefile - create new BVX file (//abandoned for now//)   * bvxcreatefile - create new BVX file (//abandoned for now//)
   * [[calcbetas]] - perform GLM regression   * [[calcbetas]] - perform GLM regression
 +  * [[cellipse]] - confidence ellipse coordinates for scatter plot
   * [[checkstruct]] - check an 1x1 struct for validity   * [[checkstruct]] - check an 1x1 struct for validity
   * [[checksyntax]] - checks a snippet of code for syntax validity   * [[checksyntax]] - checks a snippet of code for syntax validity
   * [[clearxffobjects]] - issue ClearObject call on several objects   * [[clearxffobjects]] - issue ClearObject call on several objects
   * [[clustercoords]] - get list of clusters in volume   * [[clustercoords]] - get list of clusters in volume
-  * [[clustercoordsc]] - get list of clusters in volume+  * [[clustercoordsc]] - get list of clusters in volume (//MEX file stub/help//)
   * [[clustermeshmap]] - cluster a SMP/SRF based map   * [[clustermeshmap]] - cluster a SMP/SRF based map
   * [[clustermeshmapbin]] - cluster binary mesh-based map   * [[clustermeshmapbin]] - cluster binary mesh-based map
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   * [[conjval]] - conjugate value (same sign, min abs value with sign)   * [[conjval]] - conjugate value (same sign, min abs value with sign)
   * [[conjvalp]] - conjugate pvalues (same sign, max value with sign)   * [[conjvalp]] - conjugate pvalues (same sign, max value with sign)
-  * [[conv3d]] - perform 3D convolution+  * [[conv3d]] - perform 3D convolution (//MEX file stub/help//)
   * [[convones]] - convoles a function with a number of consecutive ones   * [[convones]] - convoles a function with a number of consecutive ones
   * [[correlinvtstat]] - convert t-statistic into correlation value   * [[correlinvtstat]] - convert t-statistic into correlation value
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   * [[correltstat]] - convert correlation value into t-statistic   * [[correltstat]] - convert correlation value into t-statistic
   * [[corrmap]] - correlation map   * [[corrmap]] - correlation map
-  * [[cov_nd]] - computes covariance and corrcoefs for vector pairs in N-D+  * [[cov_nd]] - computes covariance and corrcoefs for vector pairs in N-D (//MEX file stub/help//)
   * cpfile - copies a file (//**deprecated!** use copyfile instead//)   * cpfile - copies a file (//**deprecated!** use copyfile instead//)
   * crawford_abnorm - calculate Crawford's score abnormality measure (//abandoned for now//)   * crawford_abnorm - calculate Crawford's score abnormality measure (//abandoned for now//)
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   * [[dicom4todmr]] - cheap try to convert a DICOM4 file into DMR/DWI   * [[dicom4todmr]] - cheap try to convert a DICOM4 file into DMR/DWI
   * [[dicom4tofmr]] - cheap try to convert a DICOM4 file into FMR/STC   * [[dicom4tofmr]] - cheap try to convert a DICOM4 file into FMR/STC
 +  * dicom_dic - internally used DICOM dictionary function
   * [[dilate3d]] - perform 3D dilation with operator   * [[dilate3d]] - perform 3D dilation with operator
   * [[dispslice]] - displays a 2-D dataset as an image   * [[dispslice]] - displays a 2-D dataset as an image
   * [[dispslicemovie]] - display slice movie   * [[dispslicemovie]] - display slice movie
 +  * [[dividetrimesh]] - divide triangular mesh into smaller triangles
   * [[emptysrf]] - create an empty surface container   * [[emptysrf]] - create an empty surface container
-  * [[erode]] - perform 3D erosion with operator+  * [[erode3d]] - perform 3D erosion with operator
   * [[exceltocoords]] - converts MS-Excel notation into 1x4 double array   * [[exceltocoords]] - converts MS-Excel notation into 1x4 double array
   * [[extcaller]] - from where was a call issued   * [[extcaller]] - from where was a call issued
   * [[fdr_thresholds]] - compute probability thresholds for q(FDR) levels   * [[fdr_thresholds]] - compute probability thresholds for q(FDR) levels
   * [[fendian]] - return an argument suitable for fopen (endianess)   * [[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   * [[fileguessendian]] - guess endian type of (partial) file content
   * [[filesize]] - return a file's size in bytes   * [[filesize]] - return a file's size in bytes
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   * [[findfiledir]] - find a named file or directory   * [[findfiledir]] - find a named file or directory
   * [[findfiles]] - Linux/UNIX-like find command/function   * [[findfiles]] - Linux/UNIX-like find command/function
-  * [[findfirst]] - find first (or last) element != 0 in input+  * [[findfirst]] - find first (or last) element != 0 in input (//MEX file stub/help//)
   * [[fisherr2z]] - convert Pearson correlation into z values   * [[fisherr2z]] - convert Pearson correlation into z values
   * [[fitrobustbisquare]] - faster fitting function for robust bisquare   * [[fitrobustbisquare]] - faster fitting function for robust bisquare
   * [[fitrobustbisquare_img]] - faster fitting function for robust bisquare   * [[fitrobustbisquare_img]] - faster fitting function for robust bisquare
-  * [[flexinterp]] - flexible data interpolation (up to 4D)+  * [[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_demo]] - demonstration of flexinterpn
   * [[flexinterpn_method]] - call flexinterpn with one of the typical methods   * [[flexinterpn_method]] - call flexinterpn with one of the typical methods
-  * [[flexmask]] - flexible data masking+  * [[flexmask]] - flexible data masking (//MEX file stub/help//)
   * [[floodfill3]] - keep adjacent values from seed point   * [[floodfill3]] - keep adjacent values from seed point
   * [[fmriqasheet]] - create figure with output of fmriquality   * [[fmriqasheet]] - create figure with output of fmriquality
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   * [[glmtstat]] - compute GLM t statistic   * [[glmtstat]] - compute GLM t statistic
   * [[gluetostring]] - glues a cell array of chars to one delimited char array   * [[gluetostring]] - glues a cell array of chars to one delimited char array
-  * [[gluetostringc]] - C-version of gluetostring+  * [[gluetostringc]] - C-version of gluetostring (//MEX file stub/help//)
   * gradsmooth - apply gradient based smoothing (//abandoned for now//)   * gradsmooth - apply gradient based smoothing (//abandoned for now//)
   * [[grep]] - GNU utils like grep   * [[grep]] - GNU utils like grep
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   * [[heartbeats]] - detect heart beats and frequency in physio data   * [[heartbeats]] - detect heart beats and frequency in physio data
   * [[hexdump]] - dump hexadecimal values into string   * [[hexdump]] - dump hexadecimal values into string
 +  * [[histcount]] - M-file for histcountc MEX function
   * [[hrf]] - create canonical HRF shape   * [[hrf]] - create canonical HRF shape
   * [[hrfboost]] - assume that best fit is the (root of) sum of squares   * [[hrfboost]] - assume that best fit is the (root of) sum of squares
   * [[hxdouble]] - transform a double from/into a readable string   * [[hxdouble]] - transform a double from/into a readable string
   * [[hxsingle]] - transform a single 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   * [[icc]] - intraclass correlation calculation
   * [[idftextread]] - read a text-converted IDF file (iView X)   * [[idftextread]] - read a text-converted IDF file (iView X)
   * [[image_complexity]] - give image complexity estimate   * [[image_complexity]] - give image complexity estimate
   * [[image_resize]] - resize a HxWxD numeric image to new measures   * [[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   * [[importbesa]] - import EEG/MEG data from a set of BESA files
   * [[importfif]] - import FIF file   * [[importfif]] - import FIF file
-  * [[importvtcfromanalyze]] - import an FMR from Analzye files+  * [[importfmrfromanalyze]] - import an FMR from Analzye files
   * [[importrfxglmfromspms]] - import SPM beta maps to a BrainVoyager GLM file   * [[importrfxglmfromspms]] - import SPM beta maps to a BrainVoyager GLM file
-  * [[importvtcfromanalyze]] - import several Analzye SPM map files+  * [[importvmpfromspms]] - import several Analzye SPM map files
   * [[importvmrfromanalyze]] - import a VMR from an Analzye file   * [[importvmrfromanalyze]] - import a VMR from an Analzye file
   * [[importvtcfromanalyze]] - import a VTC from Analzye files   * [[importvtcfromanalyze]] - import a VTC from Analzye files
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   * [[initialalignment]] - perform the automatic IA   * [[initialalignment]] - perform the automatic IA
   * [[invsystem]] - inverts the output argument order of system(...)   * [[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   * [[isabsolute]] - returns true if the given path is absolute
-  * [[isemptycell]] - returns a boolean array with isempty over cells +  * [[isectlp]] - compute intersection of line and plain (multi-dim) 
-  * [[isinfnan]] - checking whether (any) element(s) are inf/nan+  * [[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   * [[isrealvarname]] - true for valid variable name
-  * [[isscalarcell]] - returns a boolean array with isscalar over cells+  * [[isscalarcell]] - returns a boolean array with isscalar over cells (//MEX file stub/help//)
   * [[istransio]] - check (and validate) object   * [[istransio]] - check (and validate) object
   * [[isxff]] - check (and validate) object   * [[isxff]] - check (and validate) object
   * [[isxfigure]] - perform validity check on input   * [[isxfigure]] - perform validity check on input
   * [[isxini]] - perform validity check on input   * [[isxini]] - perform validity check on input
-  * [[joinlayers]] - joining of transimg layers into a HxWx3 image + alpha map+  * [[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   * [[kendtau]] - returns the Kendall tau statistic for two vectors
-  * [[kendtaupairsign]] - return kendall tau ties-correction value+  * [[kendtaupairsign]] - return kendall tau ties-correction value (//MEX file stub/help//)
   * [[kendtaut]] - give approximate t-score for kendall tau (via monte-carlo)   * [[kendtaut]] - give approximate t-score for kendall tau (via monte-carlo)
   * [[kendtauz]] - give approximate z-score for kendall tau (via formula)   * [[kendtauz]] - give approximate z-score for kendall tau (via formula)
   * [[kurt]] - compute kurtosis of data   * [[kurt]] - compute kurtosis of data
-  * [[limitrangec]] - limit data to a range+  * [[limitrangec]] - limit data to a range (//MEX file stub/help//)
   * [[limittorange]] - limit data to percentile range   * [[limittorange]] - limit data to percentile range
   * [[linscale]] - linear scaling transform   * [[linscale]] - linear scaling transform
   * [[lsqueeze]] - linear squeeze into Nx1 array   * [[lsqueeze]] - linear squeeze into Nx1 array
   * [[ltriasc]] - ASCII form of a lower triangle matrix (for Mx)   * [[ltriasc]] - ASCII form of a lower triangle matrix (for Mx)
-  * [[madist]] - Mahalanobis distance of single data argument +  * [[madistd]] - Mahalanobis distance of single data argument 
   * [[mainver]] - get matlab main version   * [[mainver]] - get matlab main version
   * [[makelabel]] - returns a valid label from input   * [[makelabel]] - returns a valid label from input
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   * [[meannoinfnan]] - build mean of elements other than Inf/NaN   * [[meannoinfnan]] - build mean of elements other than Inf/NaN
   * [[meanpsctrans]] - perform PSC transformation after regression   * [[meanpsctrans]] - perform PSC transformation after regression
-  * [[medianc]] - picking the median of an array using quickselect+  * [[medianc]] - picking the median of an array using quickselect (//MEX file stub/help//)
   * [[memusage]] - give the current memory usage of the calling function   * [[memusage]] - give the current memory usage of the calling function
   * [[mergehemivmrs]] - merge segmented VMRs of LH and RH   * [[mergehemivmrs]] - merge segmented VMRs of LH and RH
-  * [[mesh_morph]] -  morph the coordinates of a mesh +  * [[mesh_morph]] -  morph the coordinates of a mesh (//MEX file stub/help//) 
-  * [[mesh_trianglestoneighbors]] - get mesh neighbors list from triangles +  * [[mesh_neighborsarray]] - create a CxN neighbors list (0-filled) 
-  * [[mesh_trimapmesh]] - get triangular mapping for two spherical meshes+  * [[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   * [[minarray]] - minimize array size
   * [[minmaxbbox]] - get minimum, maximum bounding box of objects   * [[minmaxbbox]] - get minimum, maximum bounding box of objects
-  * [[minmaxmean]] - get min, max, and mean of data array (fast)+  * [[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//)   * minpos - return not the min but only the pos (//deprecated, use minmaxmean instead//)
   * [[mkadir]] - create an absolute directory (unlike to MATLAB's mkdir)   * [[mkadir]] - create an absolute directory (unlike to MATLAB's mkdir)
   * [[mltype]] - return Matlab's datatype association   * [[mltype]] - return Matlab's datatype association
 +  * [[mmregress]] - multi-model regression
   * [[mni2tal]] - converts coordinates from MNI brain to best Talairach guess   * [[mni2tal]] - converts coordinates from MNI brain to best Talairach guess
   * [[mpackage]] - MatLab Installation Package Generator   * [[mpackage]] - MatLab Installation Package Generator
   * [[mstrrep]] - replace multiple patterns (multi strrep)   * [[mstrrep]] - replace multiple patterns (multi strrep)
   * [[mtc_concat]] - concatenate MTCs   * [[mtc_concat]] - concatenate MTCs
-  * multi_voi_avg - generate Multi-VOI averaging plots (//abandoned for now//)+  * [[mtimesnd]] - mtimes (AxB * BxC) over dims 3, 4, ...
   * [[multimatch]] - match two lists of strings and return matched in first   * [[multimatch]] - match two lists of strings and return matched in first
   * [[multiset]] - set properties for multiple handles   * [[multiset]] - set properties for multiple handles
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   * [[neuroelf_gui]] - the NeuroElf graphical user interface (GUI)   * [[neuroelf_gui]] - the NeuroElf graphical user interface (GUI)
   * [[neuroelf_license]] - display NeuroElf license   * [[neuroelf_license]] - display NeuroElf license
 +  * [[neuroelf_makefiles]] - create additional files used by NeuroElf
   * [[neuroelf_makelibs]] - compile MEX functions (mex/compiler needed!)   * [[neuroelf_makelibs]] - compile MEX functions (mex/compiler needed!)
   * [[neuroelf_pack]] - create installation/update/diff package   * [[neuroelf_pack]] - create installation/update/diff package
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   * [[neuroelf_setup]] - NeuroElf post installation setup   * [[neuroelf_setup]] - NeuroElf post installation setup
   * [[neuroelf_version]] - return the version of NeuroElf   * [[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   * [[newnatresvmp]] - create natural resolution VMP object
   * [[noinfnan]] - replace Inf/NaN's in input with replacement value   * [[noinfnan]] - replace Inf/NaN's in input with replacement value
 +  * [[normcdfc]] - M-file stub for MEX file
   * [[normvecs]] - normalize vector lengths to 1   * [[normvecs]] - normalize vector lengths to 1
-  * [[num2strtab]] - creates a tabular data output of a numeric data table+  * [[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)   * [[orthimage]] - compute orthogonality matrix (for SPM like display)
   * [[orthsdm]] - orthogonalize SDM object in file   * [[orthsdm]] - orthogonalize SDM object in file
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   * [[pairs]] - returns the pairs of values in a vector/matrix   * [[pairs]] - returns the pairs of values in a vector/matrix
   * [[parseformula]] - parse a formula   * [[parseformula]] - parse a formula
-  * parsenumtable - parse a numeric table (//deprecated, use u8str2double instead//) 
   * [[parseopts]] - parse optional input arguments with defaults   * [[parseopts]] - parse optional input arguments with defaults
   * [[partoanalyze75]] - convert PAR/REC into Analyze 7.5   * [[partoanalyze75]] - convert PAR/REC into Analyze 7.5
   * [[pinvc]] - pseudo-inverse using svdc   * [[pinvc]] - pseudo-inverse using svdc
   * [[plotcurves]] - plot different curves and select those of interest   * [[plotcurves]] - plot different curves and select those of interest
-  * [[pmfilter]] - apply a poly-mask bias filter to an image+  * [[pmbfilter]] - apply a poly-mask bias filter to an image
   * pmpalignment - compute alignment PMPs (//abandoned for now//)   * pmpalignment - compute alignment PMPs (//abandoned for now//)
   * [[poolgroups]] - pool several sample groups into one stats analysis   * [[poolgroups]] - pool several sample groups into one stats analysis
   * [[prefilter]] - spike/shift/resonance filter data   * [[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//)   * progresscount - display progress in console as a step based counter (//abandoned for now//)
   * [[psctrans]] - perform PSC transformation on time course   * [[psctrans]] - perform PSC transformation on time course
-  * [[qsort]] - sorting of 1-D vectors+  * [[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   * [[ranktrans]] - return rank transform of data
   * [[rbalign]] - rigid-body alignment of one volume to a volume stack   * [[rbalign]] - rigid-body alignment of one volume to a volume stack
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   * readhrv - reads a heart rate variability text file (//abandoned for now//)   * readhrv - reads a heart rate variability text file (//abandoned for now//)
   * [[readpar]] - read a Philips PAR file   * [[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   * [[regress_coords]] - find best matching quaternion t to match coordinates
   * [[relfilename]] - build relative filename from two given files   * [[relfilename]] - build relative filename from two given files
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   * [[renamefile]] - renames a file to another filename   * [[renamefile]] - renames a file to another filename
   * render_vol - 3-D rendering of an spm_vol struct (//abandoned for now//)   * render_vol - 3-D rendering of an spm_vol struct (//abandoned for now//)
-  * [[renderlayers]] - rendering of transimg layers into a HxWx3 uint8 image+  * [[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   * [[resampleaa]] - anti-aliased resampling of data
   * [[rmean]] - re-weighted mean   * [[rmean]] - re-weighted mean
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   * [[smoothkern]] - build N-dim smoothing kernel from FWHM   * [[smoothkern]] - build N-dim smoothing kernel from FWHM
   * [[smoothned]] - smooth non-equidistant data with a gaussian kernel   * [[smoothned]] - smooth non-equidistant data with a gaussian kernel
 +  * [[smpdist]] - sample values from a discrete distribution
   * [[solvesudoku]] - solve a sudoku puzzle   * [[solvesudoku]] - solve a sudoku puzzle
   * [[spatent]] - spatial entropy of map values   * [[spatent]] - spatial entropy of map values
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   * [[splitclustercoords]] - split coords of one cluster to subclusters   * [[splitclustercoords]] - split coords of one cluster to subclusters
   * [[splittocell]] - split a delimited string into a cell array   * [[splittocell]] - split a delimited string into a cell array
-  * [[splittocellc]] - C-version of splittocell+  * [[splittocellc]] - C-version of splittocell (//MEX file stub/help//)
   * [[spm5_preprojobs]] - create jobs and jobhelps from options   * [[spm5_preprojobs]] - create jobs and jobhelps from options
   * [[spmitrf]] - uncompile an affine transformation into paramters   * [[spmitrf]] - uncompile an affine transformation into paramters
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   * srfalignment - align surface according to their folding patterns (//abandoned for now//)   * srfalignment - align surface according to their folding patterns (//abandoned for now//)
   * srfbvxalign - perform alignment of SRFs in a BVX file (//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   * [[structdiff]] - compare two structures
   * [[subclusters]] - separate mega cluster into sub-clusters   * [[subclusters]] - separate mega cluster into sub-clusters
   * [[subget]] - get a list of properties as a struct   * [[subget]] - get a list of properties as a struct
-  * [[svdc]] - singular value decomposition +  * [[svdc]] - singular value decomposition (//MEX file stub/help//) 
-  * [[svmpredict]] - train libSVM based classifier +  * [[svmpredict]] - train libSVM based classifier (//MEX file stub/help//) 
-  * [[svmtrain]] - train libSVM based classifier+  * [[svmtrain]] - train libSVM based classifier (//MEX file stub/help//)
   * [[tablesextract]] - create tables and extracts from GLM/VMPs   * [[tablesextract]] - create tables and extracts from GLM/VMPs
   * [[tal2acpc]] - convert TAL coordinates into AC-PC coordinates   * [[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   * [[tal2mni]] - converts coordinates from TAL brain to best MNI-space guess
   * tcchecksum - checksum using textcrypt (not reliable for binary data) (//abandoned for now//)   * tcchecksum - checksum using textcrypt (not reliable for binary data) (//abandoned for now//)
Line 274: Line 307:
   * [[tfgparse]] - parses a xfigure TFG file into a struct   * [[tfgparse]] - parses a xfigure TFG file into a struct
   * [[tfmatrix]] - build 4x4 transformation matrix for different steps   * [[tfmatrix]] - build 4x4 transformation matrix for different steps
-  * [[threshlutc]] - converting thresholded map to looked up colors +  * [[threshlutc]] - converting thresholded map to looked up colors (//MEX file stub/help//) 
-  * [[threshmapc]] - thresholding a double map to 0...1 +  * [[threshmapc]] - thresholding a double map to 0...1 (//MEX file stub/help//) 
-  * [[transmul]] - return the multiplication of M' * M +  * [[transmul]] - return the multiplication of M' * M (//MEX file stub/help//) 
-  * [[u8str2double]] - convert numeric text (of multi-value data) to double+  * [[u8str2double]] - convert numeric text (of multi-value data) to double (//MEX file stub/help//)
   * [[uint322colcode]] - convert from uint32 to colcode array   * [[uint322colcode]] - convert from uint32 to colcode array
   * [[unpackmosaic]] - unpack mosaic from two dimensions into third   * [[unpackmosaic]] - unpack mosaic from two dimensions into third
Line 283: Line 316:
   * [[utc]] - return utc-like time code (uint32)   * [[utc]] - return utc-like time code (uint32)
   * [[uunion]] - unsorted set union.   * [[uunion]] - unsorted set union.
-  * [[varc]] - calculation of variance along dimension+  * [[varc]] - calculation of variance along dimension (//MEX file stub/help//)
   * [[vmrspmcoreg]] - apply SPM's coregistration to two VMRs   * [[vmrspmcoreg]] - apply SPM's coregistration to two VMRs
   * [[vmvreadpos]] - read one vertex movie position in a VMV file   * [[vmvreadpos]] - read one vertex movie position in a VMV file
Line 291: Line 324:
   * writestcfiles - create STC files from a 4D array (//abandoned for now//)   * writestcfiles - create STC files from a 4D array (//abandoned for now//)
   * xffcompare - compares two xff objects (or folders with files) (//abandoned for now//)   * xffcompare - compares two xff objects (or folders with files) (//abandoned for now//)
-  * [[xffsrfparseneighbors]] - parse neighbors from SRF file +  * [[xffsrfparseneighbors]] - parse neighbors from SRF file (//MEX file stub/help//) 
-  * [[xffsrfwriteneighbors]] - write neighbors to SRF file+  * [[xffsrfwriteneighbors]] - write neighbors to SRF file (//MEX file stub/help//)
   * [[xfigurecallback]] - make sure a callback has its own workspace   * [[xfigurecallback]] - make sure a callback has its own workspace
   * [[zerodstring]] - fill a string with zero chars and fix length   * [[zerodstring]] - fill a string with zero chars and fix length
   * [[zsz]] - returns zeros(size(svzar))   * [[zsz]] - returns zeros(size(svzar))
   * [[ztrans]] - perform z-transformation on time course   * [[ztrans]] - perform z-transformation on time course
 +
 +===== Toolbox base folder, C-based functions =====
 +  * 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 functions/methods =====
 +  * [[@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 functions =====
 +  * [[@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 functions =====
 +  * [[@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 functions (besides OBJ::Method files) ====
 +  * [[@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 functions =====
 +  * [[@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 functions =====
 +  * [[@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 functions =====
 +  * [[@xprogress/xprogress]] - constructor
 +  * [[@xprogress/closebar]] - close xprogress bar and clear object
 +  * [[@xprogress/subsasgn]] - overload for subsasgn call
 +  * [[@xprogress/subsref]] - overload for subsref call
  
neuroelf_-_all_functions.txt · Last modified: 2011/04/04 20:37 by jochen