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**This is an old revision of the document!**

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!**

- Creating formula images with PhpMathPublisher (hosted locally)

- 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)
- Video tutorials (a set of screen-recordings showing various features of NeuroElf)

- Coding guidelines (
**this is IMPORTANT!!**) - Image file conversion (DICOM import, K-space reconstruction, etc.)
- 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
- Meta-analyses: Multi-level Kernel Density Analysis (MKDA)
- Output visualization: Map overlay, Montage creation (multi-slice display), Surface projection, Flatmaps
- Scripted example (taken from my lab)

- 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)
- Multi-level Kernel Density Analysis (MKDA) (Analysis menu → Meta analysis)
- Image montage UI (Visualization menu)
- Rendering UI (Visualization menu / render button)
- MDM VOI condition averages (Visualization menu)

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

- 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
- GLM methods: JoinFFX, JoinRFX, RFX_RemovePredictors, RFX_conmaps, RFX_rMap, RFX_tMap, RemoveSubject, SingleStudy_tMap, VOIBetas
- MAP methods: CreateVMP
- SMP methods: ClusterTable, Smooth
- SRF methods: AddMarkers, BackToVMR, Combine, CurvatureMap, Inflate, Morph, RecalcNormals, RecoSMToSphere, RecoToSphere, Smooth, Transform
- VMR methods: ApplyTRF, CleanVMR, CreateVTC, HiResRescale, InhomogeneityCorrect, LimitVMR, OverlayVMP, Talairach
- VOI methods: AddSphericalVOI, ApplyTrf
- 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
- 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
- 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

start.1352739480.txt.gz · Last modified: 2012/11/12 17:58 by jochen