LIPSIA   1.6     U S E R   M A N U A L
How to get started using an example data set
Example data
  • The example data set
  • The Lipsia data format
  • How to convert MRI data into the Lipsia data format
  • Standard Processing Pipeline
  • Step 1:How to transform anatomical/functional MRI data into the 3D Talairach space
  • Step 2:How to process functional MRI data in Lipsia
  • Preprocessing
  • Geometric distortion correction (vdistortionCorrection)
  • 2D Motion correction (vmovcorrection2d)
  • 3D Motion correction (vmovcorrection)
  • Slicetime correction (vslicetime)
  • Temporal and spatial filtering (vpreprocess)
  • Registration and Normalization
  • 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)
  • Statistics

    Design files
  • 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)
  • First Level Analysis
  • General linear model using precoloring (vcolorglm, vgetcontrast)
  • General linear model using whitening (vwhiteglm)
  • Second/Third Level Analysis
  • 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)
  • Region of Interest Analysis
  • 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)
  • Activation Areas
  • 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)
  • Timecourses
  • 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)
  • Visualization
  • 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)
  • Anatomical Tools
  • 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)
  • Utilities
  • 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)
  • Data Conversion
  • 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)
  • Literature
  • 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.


  • Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
    Copyright © 2008 Max Planck Institute for Human Cognitive and Brain Sciences. All rights reserved.