Welcome to the NeuroElf wiki. If you would like to contribute, please read the information provided in the wiki internals section below, register and edit/add articles! :)

Below you can find a preliminary and manually maintained table of contents. This means that in case you create a new article when you write up your own piece of documentation, please name it with a useful title, and if you consider the information you provide to be useful in a global context (e.g. a manual on how to use a specific tool or a solution to a general problem), please add the article to this page.

Once there is a sufficiently large number of articles, this will be re-organized, but for now, this should be good enough to quickly find the required information (given it is available here on the wiki).

Please note: manuals available here at the wiki mostly reflect the most up-to-date version of files available in the daily snapshot (see the main page for the link)! If a feature described therein isn't part of that last stable release, please (temporarily) use the snapshot release, if you need this feature urgently!

• Adding articles
• Creating formula images with PhpMathPublisher (hosted locally)
• Uploading image files

• Introduction (basic info, etc.)
• Installation (instructions for both installer and flat folder/snapshot ZIP)
• Compiling MEX files (some hints if compiling fails)
• Release notes (per-release list of substantial additions)
• Changelog (latest additions and changes to the snapshot of the toolbox)
• List of features (attempt at a comprehensive overview)
• Support (reporting errors and problems, feature requests)
• License and disclaimer

• Coding guidelines (this is IMPORTANT!!)
• Project folder structure
• File formats (overview)
• File transfer
• Image file conversion (DICOM import, K-space reconstruction, etc.)
• Quality assessment
• Configuration of preprocessing steps
• Recording onsets and responses
• Model-based approaches (confirmatory, hypotheses driven): Model creation, GLM regression, Contrast and correlation maps, Mediation analysis
• Model-free approaches (exploratory, covariance-based/multi-variate statistics): Cross-correlations, ICA, Mediation analysis
• Output visualization: Map overlay, Montage creation (multi-slice display), Surface projection, Flatmaps
• Scripted example (taken from my lab)

• Ajay Satpute's usage notes

• Main UI overview
• GUI menu tree
• Keyboard commands
• Loading anatomical and functional data
• GLM beta plotter (GLM menu)
• Compute multi-study GLM (Analysis menu)
• Contrast manager (Analysis menu)
• RFX (single-level) mediation (Analysis menu)
• ECG/GSR data analysis (Analysis menu)
• Image montage UI (Visualization menu)
• Rendering UI (Visualization menu / render button)
• MDM VOI condition averages (Visualization menu)
• GUI Scripting

Some of the links (questions) below have their own page, others simply re-use a wiki page that strongly relates to the topic:

• ... apply BV's alignment files (IA/FA/ACPC/TAL) to FMR space data?
• ... attach a protocol to a VTC file?
• ... assess fMRI data quality?
• ... close the GUI after accidentally clearing everything?
• ... combine VMPs with the same spatial layout?
• ... compute a conjunction map?
• ... create and combine masks (MSK) from VTCs?
• ... create activation clusters from VMP maps?
• ... create cluster tables from VMP maps?
• ... create high-resolution images of overlaid maps on slice data?
• ... display the motion parameters of a subject?
• ... extract and plot timecourse and trial-related averages?
• ... fine-tune brain segmentation?
• ... generate PRT files in Matlab?
• ... import SPM contrast maps (convert SPM t- and F-maps to VMP format)?
• ... import SPM regression results (store SPM 1st level regression output in a RFX-GLM)?
• ... import SPM timecourse data (convert SPM preprocessing output to VTC format)?
• ... perform ECG / heart-rate data analysis?
• ... perform GSR data analysis?
• ... preprocess several subjects at once using SPM5/SPM8 preprocessing?
• ... request a new feature or file format?
• ... use alphasim?
• ... use robust regression on first-level data?

• xff (main/constructor function, supported file formats, reading files, memory management)
• ROOT object methods (root.Method): ClearObjects, Document, Documents, Help
• Common methods (object.Method): ClearObject, CopyObject, DeleteHandle, FilenameOnDisk, Filenumber, Filetype, Handles, Help, Info, ReloadFromDisk, Save, SaveAs, SaveRunTimeVars, SetHandle
• 3D and 4D data shared methods (CMP/GLM/VMP/VMR/VTC; e.g. vmp.Method): Browse, BoundingBox, GetVolume, GetVolumeSize, IntensityMask, Layout, MapNames, MaskWithVMR, SampleBVBox, SampleData3D, SampleTalBox, SetOrientation, SliceData3D, SliceToTransimg
• ACQ methods: ChannelData, Filter, Resample, SampleData
• FMR methods: Filter, LoadSTC, Realign, SliceTiming
• GLM methods: JoinFFX, JoinRFX, RFX_RemovePredictors, RFX_conmaps, RFX_rMap, RFX_tMap, RemoveSubject, SingleStudy_tMap, VOIBetas
• HDR methods: LoadVoxelData, SaveVoxelData, UpdateHeader
• MAP methods: CreateVMP
• MDM methods: ComputeGLM, ConditionOnsets, SDMs, Subjects, VOICondAverage, VOITimeCourses
• MTC methods: ApplySSM, ApplyTSM
• NTT methods: ChannelData, Filter, Resample, SampleData
• PLP methods: PlotOnSlice, PlotOnSurface
• PRT methods: ConvertToMS, ConvertToSingleTrial, ConvertToVol, CreateSDM, SetDuration, ShiftOnsets
• SDM methods: AddFilters, CalcBetas, ShowDesign
• SMP methods: ClusterTable, Smooth
• SRF methods: AddMarkers, BackToVMR, Combine, CurvatureMap, Inflate, Morph, RecalcNormals, RecoSMToSphere, RecoToSphere, Smooth, Transform
• VMP methods: ClusterTable, ComputeFormula, CreateSMP, MakeHiResVMP, PerformFDR
• VMR methods: ApplyTRF, CleanVMR, CreateVTC, HiResRescale, InhomogeneityCorrect, LimitVMR, OverlayVMP, Talairach
• VOI methods: AddSphericalVOI, ApplyTrf
• VTC methods: Correlate, CreateMTC, CrossCorrelate, Filter, ICA, Resample, VOITimeCourse
• Auxiliary functions: clearxffobjects, isxff

• xfigure (main/constructor function, creating figures from TFG files, subsref and subsasgn overload to access properties)
• figure methods: hFig.SetGroupEnabled, hFig.ShowPage
• uicontrol methods: hUIC.MultiString

This section is sorted by area of application. To look up help for a specific function name, please use the Search box on top of any wiki page or look at the alphabetical function index.

• averagevmrs - average multiple VMRs into one dataset
• bcc2area - lookup labels of color codes used in BrainVoyager QX's Talairach.VMR
• createfmr - create a BrainVoyager compatible FMR object from DICOM, PAR/REC, or Analyze files
• createvmr - create a BrainVoyager compatible VMR object from DICOM, PAR/REC, or Analyze file(s)
• vmrspmcoreg - apply SPM's coregistration to two VMRs and create a TRF object

• dcm2nii - import DICOM to NIftI format (using SPM's DICOM Import tool)
• dicom2nii - import DICOM or PAR/REC to NIftI format (no SPM required)
• fmriqasheet - visualize the result of fmriquality
• fmriquality - fMRI quality assessment (per run, estimates measures of noise as well as motion and detects outliers)
• importrfxglmfromspms - import several SPM.mat files (and the used timecourses) into BrainVoyager QX's RFX-GLM format
• importvmpfromspms - import several 3D SPM based t- or F-maps into BrainVoyager QX's VMP format
• importvmrfromanalyze - import one 3D Analyze/NIftI file into BrainVoyager QX's VMR format
• importvtcfromanalyze - import several 3D or one 4D Analyze/NIftI file(s) into BrainVoyager QX's VTC format
• renamedicom - rename DICOM files (from filename list) according to a pattern using DICOM header values (incl. UI)

• solvesudoku - Sudoku puzzle solver (not the best one, but it works)

• acsvread - read CSV (comma-separated-value) files (e.g. text-based Excel sheets)
• findfiles - seek file/folder names in filesystem, create list of filenames with pattern for scripted processing
• qsort - C-based Qsort algorithm (only for certain applications
• u8str2double - parsing large text files with tabular numeric data (MEX file: fast)

• flexinterpn and the more user friendly flexinterpn_method - flexibly interpolate data (up to 4D)
• resampleaa - resample data with anti-aliasing (uses flexinterpn but has different option set, also distinguishes better between up- and downsampling)

• computehrv - compute heart-rate variability (HRV) from onset data
• heartbeats - detect and visualize heart beats from ECG recording (incl. manual de/selection of problematic beat locations)
• plotcurves - flexibly visualize curves and, if requested, determine points of interest (e.g. peaks) and compute distances (response times, amplitudes, etc.)
• prefilter - pre-processing filter of signal data (removal of unwanted frequencies, resonance, and noise components)

• fitrobustbisquare - robustly fit (weighted) least-squares model by iteratively re-weighting outliers using the bisquare function
• fitrobustbisquare_img - apply robust fit on multi-dimensional data, instance-by-instance (faster than looping around fitrobustbisquare)

• clustercoords and clustercoordsc - cluster coordinates in 3D data volume
• clustermeshmap and clustermeshmapbin - cluster coordinates on 2D mesh surface
• clustervol - cluster binary volume (used by clustercoords)
• conv3d - C-based 3D spatial convolution
• splitclustercoords - attempt to split a cluster into sub-compartments using a modified watershed algorithm

• acpc2tal - apply BrainVoyager TAL transformation to coordinates
• applybvtrf - apply BrainVoyager TRF transformation to coordinates
• bvcoordconv - convert between TAL/MNI space and diverse BrainVoyager QX spaces (interal/external/voxel coordinate systems)
• bvtrf - compile BrainVoyager QX compatible transformation matrix (see also TRF object)
• mni2tal - apply Matthew Brett's coordinate conversion from MNI to Talairach space
• tal2acpc - apply inverse BrainVoyager TAL transformation to coordinates

• alphasim - simulate random data/maps to determine cluster level threshold under given smoothing conditions
• calcbetas - perform ordinary least-squares (OLS) regression and, if requested, compute predicted time course and SE
• conjval and conjvalp - compute conjunction of statistics (where conjvalp inverts the min to a max logic for signed, one-tailed p-values)
• correlinvtstat, correlpvalue, and correltstat - convert correlation coefficient ® from/into t-statistic (or p-value)
• corrmap - correlation map with support for OLS, robust regression, and Kendall Tau coefficient
• cov_nd - compute covariance/correlation arrays over last dimension of N-dimensional data
• custom_pwelch - compute Welch's method periodogram over data
• kurt - kurtosis
• sdist - statistical distributions (one function, e.g. Fcdf, tcdf, tinv, etc.)
• skew - skewness
• varc - C-based variance (faster for single-core processing)

• psctrans - per cent signal change (%) transformation (incl. applying transform in one dimension for multi-dimensional data)
• tempfilter - apply temporal filtering to (multi-dimensional) data
• ztrans - z-transformation (incl. applying transform in one dimension for multi-dimensional data)

• colorpicker - select color(s) from RGB/HSV color space

• afni_parse - AFNI's HEAD format parser (used by xff)
• analyzetype - return datatype for internal use by the Analyze/NIftI format
• any2ascii - converts other datatypes into ASCII representation (for storage in text files and use with eval)
• asciiread and asciiwrite - read/write file contents as ASCII (handle line breaks)
• barycoord - compute barycentric coordinates
• binread and binwrite - read/write file contents as uint8
• checkstruct - compare struct with well-formated list of fields and options
• checksyntax - detect syntax errors in code without actually running it (uses eval)
• colcode2uint32 and uint322colcode - internal routine to convert the color coding used in BrainVoyager's SRF format
• convones - convolve a given vector with an all-ones vector of given length
• filesize - get size of given filename in bytes

• Using dbstop to locate errors
• Checking xff files for problems
• Reporting an error with NeuroElf