bvqxtools.m

toolbox of BVQX, This is the access between BV and matlab. It will help you to analysis data from BV

% BVQXtools
%
% Matlab toolbox developed, written and maintained by Jochen Weber
% with the help and inspiration of
%
% - Hester Breman, Brain Innovation, B.V.
% - Federico Demartino, Brain Innovation, B.V.
% - Fabrizio Esposito, Brain Innovation, B.V.
% - Elia Formisano, Faculty of Psychology, University of Maastricht
% - Rainer Goebel, Faculty of Psychology, University of Maastricht
% - Armin Heinecke, Brain Innovation, B.V.
% - Pim Pullens, Brain Innovation, B.V.
% - Alard Roebroeck, Faculty of Psychology, University of Maastricht
%
% (c) 2003 - 2007, Brain Innovation, B.V., Maastricht, NL
%
% classes:
%
% @BVQXfile     - class to allow file I/O of BrainVoyager QX files
% @BVQXprogress - simple progress bar for scripts / methods
% @transio      - transparent IO access into binary files (memory saving)
%
% mainly used scripts/functions:
% bffdocu   - BFF documentation (help m-file)
% bffio     - read/write binary file (BVQX) according to spec
% bffparse  - parse BFF specification to struct (please see bffdocu)
% dcmio     - read DICOM files
% ioidx     - convert indexing subscripts to indices
% tffdocu   - TFF documentation (help m-file)
% tffio     - read/write text file (BVQX) according to spec
% tffparse  - parse TFF specification to struct (please see tffdocu)
%
%
% auxiliary scripts/functions: (adapted from other toolboxes)
%
% acpc2tal        - convert ACPC based coordinates to TAL
% acsvread        - read tabular ASCII file into cell/struct array
% analyzetype     - resolving Analyze datatypes
% any2ascii       - convert datatypes into ascii representation
% applybvtrf      - apply one of BV's 4x4 TRF matrices to coordinates
% asciiread       - read a ascii text file into a 1xN char array
% asciitab        - create custom ASCII file of 2D double array
% asciiwrite      - write a ascii text file from a 1xN char array
% averagevmrs     - build an average of a list of VMRs
% binread         - read a binary file into a 1xN uint8 array
% binwrite        - write a binary file from a 1xN char/uint8 array
% bitdump         - dump 8-bit bitfield of uint8 array
% bv2tal          - convert BV-system to TAL style coordinates
% bvcoordconv     - conversion chain between different systems
% bvtrf           - compute TRF matrix from 3D volume tools values
% checkstruct     - check and populate structures
% checksyntax     - find basic errors in code
% clearbvqxobjects - clear the passed objects from the global storage
% clustercoords   - cluster a list of coordinates
% convones        - convolute a vector with an all-1's vector
% correlpvalue    - convert an r into a p value
% correltvalue    - convert an r into a t value
% cov_nd          - calculate covariance on N-D matrices
% cpfile          - copy a file with IO
% createvmr       - create a VMR object from DICOM or PAR/REC files
% custom_betacdf  - beta CDF
% custom_betainv  - inverse of beta distribution function
% custom_betapdf  - beta PDF
% custom_fcdf     - F CDF
% custom_finv     - inverse of F distribution
% custom_fpdf     - F PDF
% custom_tcdf     - t CDF
% custom_tinv     - inverse of t distribution
% custom_tpdf     - t PDF
% dicom4tofmr     - convert a 4D DICOM file to FMR
% dispslice       - display 2-D data as image
% dispslicemovie  - display a 3-D array as series of images (movie)
% emptysrf        - create a truly empty SRF
% exceltocoords   - get numeric coords from excel range string
% extcaller       - get name of file calling the caller
% fdr_thresholds  - compute FDR thresholds for MCP
% fileguessendian - guess endianness of file
% filesize        - get filesize
% fileswapendian  - swap endianness of file
% findfiledir     - find a named file or directory
% findfiles       - find files in a path (dir search)
% fisherr2z       - apply Fisher z-transform on r values
% gammapdf        - return gamma PDF for X, h, l
% glmtstat        - compute GLM t statistic
% gluetostring    - create a CSV list from a cell array
% grep            - Linux/Unix like grep command for files/strings
% gzip            - gzip function hub
% hasfields       - checks a struct if it (only) has certain fields
% hexdump         - hexdump of uint8/char/double content
% hrf             - calculate canonical HRF (single- or two-gamma)
% hxdouble        - internal double representation (hex)
% hxsingle        - internal single representation (hex)
% initialalignment - compute IA matrix from FMR/VMR headers
% invsystem       - inverse system output arguments order
% ioidx           - give continuous indices for IO operations
% isabsolute      - check paths for absolute content
% isrealvarname   - check whether a string is a varname (enhanced)
% ltriasc         - ASCII form of a lower triangle matrix (for Mx)
% mainver         - return MATLAB main version (for compatibility)
% makelabel       - make a label from a string
% mavg            - calculate moving average
% md5sum          - md5sum function hub
% minarray        - minimize array with thresholds
% minmaxbbox      - generate minimum and maximum bounding boxes
% mkadir          - make all dir (incl. parents)
% mni2tal         - convert MNI to TAL space coordinates
% mstrrep         - apply strrep multiple times
% multiset        - set properties for multiple handles
% multislicetovol - convert a multislice raw image to an img/hdr vol
% multi_voi_avg   - multi-VOI-average
% newnatresvmp    - create empty NR-VMP
% orthimage       - return orthogonality image (scaled 0 .. 1)
% orthrtc         - orthogonalize an RTC object
% orthvec         - orthogonalize vectors
% orthvecs        - orthogonalize set of vectors
% ostype          - general hub for OS specific tests
% osz             - ones with the size of the input argument
% parseopts       - parse options (varargin)
% progresscount   - progress counter (console)
% psctrans        - percent signal transformation
% randm           - random numbers from different distributions
% readpar         - Philips PAR/REC reader
% reframearray    - place N-D field in new limits
% relfilename     - build relative filename
% renamefields    - rename fields in a struct
% renamefile      - lazy file renaming
% samplefmrspace  - sample BV's FMR space at given coordinates
% splittocell     - split a CSV list into a cell array
% spmmat2prt      - convert SPM2 design matrix into a PRT
% spmmat2rtc      - extract RTC from SPM2 design matrix
% subget          - get a (sub) list of properties as a struct
% tal2acpc        - convert TAL coordinates to ACPC space
% tal2bv          - convert TAL style to BV-system coordinates
% tdclient        - neat interface to tdlocal/2
% tdlocal         - local TD client (old version)
% tdlocal2        - local TD client, based on v2.0
% tfmatrix        - create 4x4 transformation matrices
% unzerostring    - remove trailing zeros from string
% uunion          - unsorted union
% vtc_concat      - concatenate VTCs
% writestcfiles   - create STC files from a 4-D array
% zerodstring     - create zero padded string
% zsz             - zeros with the size of the input argument
% ztrans          - z transformation

% Version:  v0.7c
% Build:    7100308
% Date:     Oct-03 2007, 8:14 AM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools