Lipsia User Manual

Geometric distortion correction (vdistortionCorrection)

2D Motion correction (vmovcorrection2d)

3D Motion correction (vmovcorrection)

Slicetime correction (vslicetime)

Temporal and spatial filtering (vpreprocess)

Obtaining the transformation matrix (vreg3d)

Spatial linear normalization (vnormalize)

Checking the registration by applying the transformation matrix (vdotrans)

Applying the transformation matrix to functional data (vfunctrans)

Spatial non-linear normalization (vdemon,vdeform)

Design file format (design format)

Generating design files (vgendesign,vaddcovariates)

Concatenating design files for fixed effects analysis(vcatdesign)

Checking the design matrix (vcheckdesign)

Generate randomized designs (vmetropolis)

Convert onset vectors to lipsia format (vspm2lipsia)

General linear model using precoloring (vcolorglm, vgetcontrast)

General linear model using whitening (vwhiteglm)

Regression for higher level inference(v2ndlevel)

One-sample t-tests (vonesample_ttest)

Two-sample t-tests (vtwosample_ttest)

Paired t-tests (vpaired_ttest)

Bayesian second/third-level analysis (vbayes,vbayesgroup)

Wilcoxon test (vwilcoxon)

Conjunction analysis (vnumave)

Interactive segmentation and drawing of ROIs (vledit)

Offline definition of ROIs (vmaskedit)

One-sample t-tests in ROIs (vROIonesample_ttest)

Two-sample t-tests in ROIs (vROItwosample_ttest)

Paired t-tests in ROIs (vROIpaired_ttest)

Wilcoxon test for matched pairs in ROIs (vROIpaired_wilcoxtest)

Report ROI-based average contrast values (vmaskave)

Average and PCA of fMRI time courses within ROIs(vtc)

Computing the false discovery critical height threshold (vfdr)

Multiple comparison correction using single thresholding (valphasim)

Multiple comparison correction using double thresholding (vmulticomp)

List of activations areas (vblobsize)

Thresholding statistical maps (vpretty)

Local activation maxima (vzmax)

Display list of coordinates (vshowpts)

Trial averages of fMRI time courses (vtrialaverage)

Parameters of average time courses (vimagetimecourse,vdifftimecourse,vextractparam)

Correlation and PPI analysis (vlcorr,vgetcovariates)

Spectral analysis of fMRI time series (vspectral)

Orthogonal cross sections of several data sets (vlv)

Orthogonal cross sections, time courses, fitted response, and sulci (vlview)

A simple viewer for anatomical and functional data (vsview)

Display raw data using orthogonal cross sections (vqview)

Display outlines of activation areas of several zmaps (vzmapborder)

Interactive 3D Renderings (vlrender)

Apply a brain mask to an activation map (vbrainmask)

Identification of AC and PC (vcacp)

Transformation into Talairach space and Brain peeling (vtal)

Brain peeling (vbrainpeel)

White matter segmentation (vwhitematter)

Extracting the cerebellum in a white matter segmentation (vdelcereb)

Sulcal lines (vsulcogram)

Group average (vave)

Selection of a range of timesteps from an fMRT time series file (vseltimesteps)

Select a single timestep from an fMRT time series file (vtimestep)

Convolution with a Gaussian filter or its derivative (vgauss)

Masking images (vimagemask)

Scaling to a new voxel resolution (vmapscale)

Changing header entries (vattredit)

Copying header entries from one image to another (vattrcopy)

Removing header entries to make data set anonymous (vanonym)

Transpose and resample a 3D dataset (visotrop)

Conversion of Bruker data to Vista (brutov2)

Conversion of Siemens Trio data to Vista (dictov)

Conversion of NIfTI images to Vista and vice versa (niftov,vtonifti)

Conversion of Analyze images to Vista and vice versa (anatov,vtoanalyze)

Lohmann G, Mueller K, Bosch V, Mentzel H, Hessler S, Chen L, Zysset S, von Cramon DY. 2001. Lipsia - A new software system for the evaluation of functional magnetic resonance images of the human brain. Computerized Medical Imaging and Graphics 25(6): 449-457.