BrainVoyager Support

documentation overview

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5/6/2010, v0.8d
added ICA functionality (re-using Aapo Hyvarinen's FastICA code with permission)
new objects: PLP (plotting points)
new methods: FMR::CrossCorrelate, GLM::RFX_conmaps, PLP::PlotOnSlice, PLP::PlotOnSurface, VMP::ComputeFormula
new functions: autocorr (auto-correlation), kurt (kurtosis), linscale (min/max linear scale), sdist (replacing the custom_* cdf/inv/pdf functions), skew (skewness)
bug fixes: MDM::ComputeGLM now sets the correct transformation value (1 or 3)

3/19/2010, v0.8c
removed the GUI class/tool (specialized visualization tools might be introduced again later)
added the .RunTimeVars construct to allow persistent storage of additional information per object
support for computing RFX-GLMs from MDMs with robust regression (takes quite long!), also supports transparent SDM-creation from PRTs
new functions/methods: GLM::ConvertToVMP (only for RFX GLMs for now), VMP::ComputeFormula,
enhanced functions: alphasim (now allows to estimate false-positives for given maps of a 2nd level correlation), renamedicom
bug fixes: PRT::ConvertToMS, SMP::ClusterTable, fmriquality (much lower memory requirements), isinfnan (MEX, only worked for some platforms)

11/23/2009, v0.8b
significantly extended the BVQXtool (GUI) class to allow several maps overlay, cluster table, tdclient, alphasim integration
got the @transimg class to do something useful (blending several images with alpha channel)
created a graphical installation output (splash screen)
some initial work on GUI functionality (alphasim, tdclient, importrfxglmfromspms)

10/17/2009, v0.8a
added file format: COV (COVariate files), HEAD (AFNI HEAD/BRIK, read-only) 
patched file formats: MAP (DF1/DF2), PRT (Parameters)
added/patched methods: AFT::Help, FMR::CrossCorrelate, GLM::RFX_RemovePredictors, GLM::RFX_tMap, PRT::CreateSDM, ROOT::Document, ROOT::Documents
new function: fmriquality (assessing the quality of fMRI data, still under development!)
re-written bvqx_srf_parseneighbors and bvqx_srf_writeneighbors in C (approx. 10 times faster SRF file access)
patched functions: calcbetas, glmtstat
some minor corrections with some functions

7/31/2009, v0.7g 
patched file formats to reflect changes made in BVQX v2.0.x 
some minor corrections with some functions

11/5/2008, v0.7f
corrected the current affiliation of the main author in newer files
added functions: flexinterpn (MEX), gluetostringc (MEX), splittocellc (MEX)
added method: GLM::RFX_rMap to generate OLS and robust regression correlation maps
some minor corrections with some functions and added help for MEX functions

10/18/2008, v0.7e
cleaned a lot of functions and speeding up things with profiler
added file format: SPSS (allows to write SAV files)
added functions: alphasim, bvqxfilehead, clustercoordsc (MEX), clustervol, smoothdata3, splitclustercoords
added methods: GLM::JoinRFX, GLM::PlotBetas, SPSS::ImportData

6/18/2008, v0.7d, release with BrainVoyager QX v1.10 file formats
updated/added file formats: ATD, CMP, GAL, GLM, SDM, SMP, VMP
updated/added functions: acsvread, createsrf, cutnpastemovie, depcorrt, scaleimage, smoothest3d, spherecoords, spherecoordsinv
updated/added methods: AFT::BoundingBox, AFT::DeleteHandle, AFT::Handles, AFT::SetHandle, SRF::CreateVMVFromMTC, SRF::CreateVMVFromSMP, VMP::ClusterTable

10/3/2007, v0.7c, release with split binary files folder
binary files moved to their own folder (simplifying snapsnot handling)
some functions removed (to protect Brain Innovation's business interest)
new functions: importvmpsfromspms, spherevmr
new methods: SRF::DensityMap, VMP::ImportSPMMaps, VTC::CrossCorrelate
added files: colin.vmr (used to overlay resampled SPM results in BV), colin_RH.srf, colin_LH.srf + transformation files (used to create surface results of SPM maps)

9/7/2007, v0.7b, release with new memory management scheme
new file formats: ATD, BSA
updated / tested formats: DMR, DWI, FMR, HDR, MAP, SFH
new classes: @BVQXfigure (general figure/ui class), @BVQXinifile (config file handling), @BVQXprogress (simple progress bar), @BVQXtool (GUI)
new methods: AFT::BoundingBox, AFT::GetVolume, MAP::CreateVMP, VMP::ClusterTable, VMP::ConvertToNatRes, VMP::MakeHiResVMP, VMR::CleanVMR, VMR::CreateVTC, VMR::OverlayVMP, VMR::SetConvention, VOI::ApplyTrf
new functions: acpc2tal, applybvtrf, applyfdr, averagevmrs, bvcoordconv, clustercoords, correlinvtstat, correlpvalue, correltstat, dilate3d, erode3d, fileswapendian, fisherr2z, floodfill3, importvtcfromanalyze, initialalignment, orthimage, samplefmrspace, spmmat2rtc, transio::resolve
improvements: memory management centralized to allow call-by-reference, including garbage collection of subfunctions

7/20/2007, v0.7a, re-release
service patch to get transio access working again from within BVQXfile

7/17/2007, v0.7a, release for BVQX v1.9 (new file formats)
new file formats: CPS, DDT, FIF, GRB, SFH
updated / tested formats: DMR, MAP, VMP, VMR
new methods: FIF::*, POI::Area, PRT::ImportStimChannels, SRF::RecalcNormals, VMP::Update
new functions: fdr_thresholds, fifio, ima2v16, renamefile, spmmat2prt
improvements: more efficient cache of FileFormat information in BVQXfile class, transio class is now fopen save (Matlab R14SP2)

6/19/2007, v0.6f, again minor amendments and additions
new file formats: DMR, DWI, EIG, VGD
new methods: GLM::RFX_RemovePredictors, MTC::SmoothIterativeNN, VTC::Resample
new functions: orthrtc, readbesa
minor bug and format fixes in a few formats, functions, and methods

3/2/2007, v0.6e, rather only minor amendments and additions
transio read support for Matlab v6.5
added function: ltriasc (get ASCII output of lower triangular matrix for Mx)
added method: GLM::RFX_tMap (currently only for MTC-based RFX GLMs)
some minor format/bug fixes

2/7/2007, v0.6d, UFF file format, file selection and spec caching feature for BVQXfile and new methods, functions + bug fixes
UFF file format added
added file selection to BVQXfile: v = BVQXfile('*.vmr');
specifications are cached for faster BVQXfile access
new methods: AVG::Average, AVG::Plot, GLM::SingleStudy_tMap, SRF::FindSpikes, VOI::BVCoords, VTC::CreateGLM, VTC::VOITimeCourse
new functions: orthvecs, glmtstat, mx, mxgrep, parrecvmr, writestcfiles
bug fixes in several formats and functions

1/12/2007, v0.6c, several smaller bug fixes, new file formats and methods
bug fixes in formats: CMP, SRF, SSM, VMV
most file formats now support creation from scratch
new methods: Any::Help, CMP::AddComponent, DTSF::SaveAsFBR, PRT::ConvertToMS, PRT::ConvertToVol, PRT::CreateRTC, VMP::SaveAsVMR, VVD::CalcROIBetas
extension ICA is now supported (as CMP)
new functions: convones, gammapdf, hrf, mx, orthvec

12/20/2006, v0.6b, two new file formats: OLT, POI; fixed some bugs, etc.
new file formats: OLT (lookup table for colors) and POI (patch of interest)
bug fix: file formats that transposed a matrix would do so on save (rendering the contents useless)
enhanced SRF::Show method, now colors are displayed as in SRF, also support for SMP overlay

12/13/2006, v0.6a, added @transio class
new class: transio, adds transparent access into binary files (VTC, MTC, GLM) for less memory consumption

12/4/2006, v0.5c, added own DICOM reader, some new formats and methods
new functions: dcmio, psctrans, tdlocal2 (based on v2.0), ztrans
new formats: DCM, VVD, VWP
new methods: GLM::JoinFFX, GLM::PSCMaps, PRT::CleanUp, SRF::Show, VMP::SaveSubset, VTC::MeanStd

11/21/2006, v0.5b, some fixed and speedups
new function: tal2bv
improved functions: bv2tal, tdlocal (speedup)

11/19/2006, v0.5a, many fixes and additions
new/improved file formats: CTR, FBR, FDP, GRAD, HDR, MDM, ROID, TDMC, TMV, TVL, VMR
new functions: tdclient, tdlocal
improved functions: splittocell (much more efficient)

11/3/2006, v0.4a, create new files, full class interface
full class interface (overloaded methods to remove BVQXCONT, etc.)
implemented consistency check feature
added creation of emtpy files feature
fixed AVG.tff (Event-related averaging files, thanks to Erik Chang)

10/4/2006, v0.3a, corrected some of the BFF files
fixed GLM.bff (DesignMatrix was read with columns and rows swapped)
fixed MSK.bff (older MATLAB version < 7 would give a warning)

9/13/2006, v0.2a, first public release