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BrainVoyager Available Tools Matlab Tools Functions in NeuroElf (BVQXTools)

Functions in NeuroElf (BVQXTools)

For your convenience, a number of additional function are part of the toolbox, of which a few shall be explained here:

  • acpc2tal - converts BV system coordinates from ACPC space into TAL space (with the respective TAL information), or inverse
  • acsvread - reads in tabular data, can be used for virtually all tabular text files, including header skipping and column naming
  • any2ascii - converts virtually any datatype into an ASCII representation that is usable for a call to eval
  • applybvtrf - applies a BV transformation matrix to a coordinate list (or inverse) applyfdr - gives the threshold of an applied FDR to either t,F,r or p statistic (in the input statistic type)
  • averagevmrs - averages a list of VMRs (supports unmatching dimensions, either in a minimum or maximum containing box)
  • bv2tal - converts the BV internal system coordinates into TAL compliant ones
  • bvcoordconv - aplly the transformation chain: TAL - BVSys - BVInt - matrix subscripts - matrix indices (or reverse)
  • bvtrf - compile a BV-compliant TRF matrix from translation and rotation parameters
  • clearbvqxobjects - clears a list of objects from the global storage
  • clustercoords - returns the list of coordinates of clustered sub-volumes correlpvalue - converts a correlation value to p (correltstat and correlinvtstat can be used to convert r to t and back)
  • convones - fast convolutes the given vector with a all-1's vector of given length
  • createvmr - similar to BrainVoyager project creation, a VMR object will be created from DICOM, PAR/REC or Analyze files
  • custom_tpdf, etc. - custom versions of distribution functions often needed for fMRI-based statistics (F, t, beta distributions); copies from free-of-charge libraries
  • dispslicemovie - internally uses dispslice to visualize a 3D dataset as a series of slices that are scanned through, one by one
  • emptysrf - create an empty surface file
  • fdr_thresholds - finds FDR thresholds for given set of p values
  • fileswapendian - swaps (part of) a file in endian type (with configuration wordsize)
  • findfiles - Linux/Unix like function for the GNU find command
  • fisherr2z - convert Fisher's correlation coefficient to z-value (or inverse)
  • gluetostring - takes a cell array of strings and returns a 1xN char array made up from the single strings put together by some glue
  • grep - Linux/Unix like function for the GNU grep command
  • hrf - returns the (configurable) canonical HRF shape
  • hxsingle / hxdouble - convert a single/double numeric into an exact ASCII representation and back
  • importvtcfromanalyze - import an MNI space Analyze time series as VTC
  • initialalignment - compute BV's initial alignment matrix from VMR/FMR headers
  • interpn_linnonull - (Tri-) Linear interpolation of data where 0 is treated as missing sample
  • makelabel - create a usable label from a given string
  • md5sum - compute MD5 checksum over file or char array
  • minarray - remove all null slices of an array
  • mkadir - absolute version of mkdir command/function
  • mni2tal - Matthew Brett's function to convert from MNI space to TAL
  • mstrrep - multiple replacements within strings
  • newnatresvmp - create a new, standard space, natural resolution VMP object, as the default is still old, 1x1x1mm VMP for BVQXfile('new:vmp');
  • orthimage - return an image (scaled 0 to 1) for the design's pairwise orthogonality (as in SPM) orthvec / orthvecs - regressor orthogonalization
  • psctrans - percent signal change transformation of time course data
  • readpar - reader for Philips PAR/REC files
  • samplefmrspace - sample BV's FMR space (differing from VMR system coordinates!)
  • splittocell - split a 1xN char array to a list of strings
  • spmmat2prt - convert an SPM2/5 design matrix into a BVQX PRT file
  • spmmat2rtc - convert an SPM2/5 design matrix into a BVQX RTC file
  • tdclient - perform a request to a (local) Talairach Daemon database (local version implemented in tdlocal or tdlocal2)
  • tfmatrix - create a transformation matrix (quaternion) from translation, rotation, scaling and shearing parameters
  • vtc_concat - concatenate VTCs (in time), uses transio and allows large files
  • ztrans - z-transformation of time course data
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