Here we present the Brain Image Analysis Package (BIAP), a software package for editing, viewing and analysis of multi-model brain images and signals. The package consists of two main programs, BIAP1D, which is meant for MEG and EEG data sets and BIAP4D, which is meant for 3D and 4D scans as MRI, fMRI, CT, PET as well as 3D markers, dipoles, delineations and surfaces. This software is offered to the scientific community for non-commercial and non-clinical purposes.
BIAP was built as spin-off of many brain brain imaging research projects led by Dr. JC de Munck and his collaborators. The software can be downloaded here or it can be obtained by sending a request to jc.munck@vumc.nl.

Coming up:
ICA analysis in BIAP1D
Linux Version



Latest Version: 1.60


BIAP4D version 1.60
Updates: 

• Several bug fixes
  

BIAP1D version 1.60
Updates:

• Bug Fix: single channel view for ANT data,
• Improved functionality for single channel view of MEG/EEG data,
• Improved functionality outlier detection.
  

BIAP4D version 1.52
Updates: 

• Removed center shift when reading DICOM files as reference scan
• Added power point slides explaing how to find electrode positions from gel artefacts
• Close all windows after closing program (bug fix)

BIAP1D version 1.52
Updates:

• Improved marker manipulation (creating equidistant events),
• Improved auto-scaling of MEG/EEG maps,
• Improved support for TMSI data format (recognizing standard electrodes).
• Close all windows after closing program (bug fix)
  

BIAP4D version 1.51
Updates: 

• No substantial functional updates since last version
  

BIAP1D version 1.51
Updates:

• Improved marker manipulation (splitting events in subgroups),
• Detecting good epochs (in addition to BAD epochs),
• Avoid overflow errors when writing EEG data as EDF,
• Extended options to present overlays of different data sets.
  

BIAP4D version 1.48
Updates: 

• Saving annotated points in VTK format
  
• Improved reading of DICOM files

BIAP1D version 1.48
Updates:

• No substantial functional update since last version

BIAP4D version 1.45
Updates: 

• No substantial functional update since last version
  

BIAP1D version 1.45
Updates:

• Sorting channels alphabetically
• Making maps over overlaid MEG/EEG data
  

Bug fixes:

• Reading vectorized data for BrainVision data files
  

BIAP4D version 1.41
Updates: 

• Tool for annotation of point lists
  
• Optimized presentation of (microscopic) 3D tif files
  

BIAP1D version 1.41
Updates:

• Suppression of 60 Hz powerline noise (in addition to 50 Hz)
  

Bug fixes:

• Button for deleting middle events (all except first and last) did not work properly
  

BIAP4D version 1.40
Updates: 

• Simplify creation of MEG/EEG forward models
• Optimize algorithm for scan template formation from surfaces
• Added option to fit shape on point list (e.g. fit MEG/EEG forward model on electrode positions)
• Extended marching cubes settings (triangulating background)
  

BIAP1D version 1.40
Updates:

• Reading GDF data format
• Improved BEM algorithm
  
• Improved 3D headmodel visualisation
• Automatic selection of channels from previous session (using .skptxt file)
• Improved event marker manipulation (e.g. splitting ANT triggers in different subsets)
  

BIAP4D version 1.22
Updates: 

• Improved import of multiple reference scans
  

BIAP1D version 1.22
Updates:

• Reading ANT 64 bits format

BIAP4D version 1.21
Updates: 

• Import of FreeSurfer and .vtk files
  
• Export .vtk files
• Distance Transform, kernel based histogram equalization
  

BIAP1D version 1.21

Updates:

• Computing spatio-temporal covariance matrix (Kronecker product model)
  

BIAP4D version 1.17
Updates: 

• Upgraded to Qt_4.8.6
• Added watershed filter.

BIAP1D version 1.17
Bug fixes:

• Reading EDF files.
• Reading ANT 256 channel data (recognizing EEG channel labels)
  

Updates:

• Upgraded to Qt_4.8.6

BIAP4D version 1.16
Updates: 

• Added Sauvola filter.

BIAP1D version 1.16
Bug fix:

• Reading EDF files with asymmetric scaling (offset was erroneously omitted).

BIAP4D version 1.15
Bug fix:

• Several (minor) bug fixes related to annotated point lists.
• Changes in reading Nifti files
  

BIAP1D version 1.15
Updates:

• Reading .evl event files associated with Elekta`s Fif-format.
• Added new functionality to view and analyse spectrograms, e.g. extracting frequency band regressors.
• Improved colour scales in level/window dialogue box.

BIAP4D version 1.13
Bug fix:

• Applying connected component analysis on binary images did not work on Win64.

BIAP1D version 1.12
Bug fix:

• Reading BrainProduct files, binary version.

BIAP1D version 1.11
Bug fix:

• In older versions BCG correction did not correctly apply the overlapping window algorithm.

Updates:

• Integration of physiological log files during fMRI artefact correction,
• Improved algorithm for slice timing parameters (time to slice and slice time),
• Addition of standardized marker file in text format (extension .mrktxt). This file is automatically read when a data file is opened and events are imported.

BIAP4D version 1.11
Updates:

• Improved treatment of Nifti files (scan orientation),
• Recognition of multiple slices in .tif files (now treated as 3D scans),
• Possibility to split scans into multiple vector components.

BIAP1D, sketched above, is a complete MEG/EEG data editor and includes the following features:

Imported data formats

• CTF(*)
• TMSI
  
• Elekta FIF
• MicroMED
• Neuroscan
• BrainAmp
• BioSemi
• ASCII(*)
• ANT
• EDF(*), EDF-plus
• GDF (2.0)
  
• Philips, GE and Siemens physiologically log files

(*) Import and export.


Event editor

• Manual/automatic editing
• Template matching
• Event density plots (to be used with co-registered fMRI)
• Import/export of events
• Event clustering
• Selective averaging

Dipole modelling

• Moving and stationary dipoles
• Coupling multiple data sets or conditions
• Realistic models, anisotropic multi sphere models
• Spatially and/or temporally correlated noise models
• Confidence intervals
• Global search algorithm
• Signal space projection

FMRI artefact correction

• Gradient artefacts
• Pulse artefacts
• Clustering, selective averaging, template estimation
• Synchronization of externally recorded ECG/respiration data
• Creation of EEG-based fMRI-regressors
  

Correlation analysis

• Cross spectra/ power spectrum
• Wavelet analysis, spectrogram computation
• Synchronization likelihood
• Coherence analysis
• EMG/MEG EMG/EEG correlation analysis
• Channel clustering
• Bad-channel bad epoch detection

Visualisation

• Maps of EEG/MEG events or power spectra
• Spectrogram
• Correlations
• Event density
• Overlay of multiple EEG/MEG data sets
• Sleep scoring

BIAP4D, shown above is 3D/4D Data Viewer with the following features:

Imported data formats

•  DICOM(*)
•  CTF SAM and MRI data
•  Elekta FIF Beamformer and MRI data
•  PET Matrix format(*)
•  Analyze and Nifti 3D and 4D format(*)
•  Philips PAR/REC
•  AFNI 1D, 3D and 4D format
•  InterFile
•  AVS-data format(*)
•  Native data format(*)

(*)Import and export.

Image analysis

•  Automatic/marker/manual image matching
•  Motion correction
•  Image segmentation/filtering
•  Brain atlas overlay
•  Landmark/dipole/annotated points (electrodes/ CTF and FIF dipoles/ FIF digitization points)
•  Min/max detection
•  Connect components

fMRI analysis

•  Regression analysis
•  Regressor manipulation/filtering
•  Multiple comparison correction (using false detection rate)
•  Hemodynamic response estimation (with confidence intervals)
•  Slice time correction
•  Clustering analysis
•  Electrode detection/labelling

Geometrical modelling

•  Surface creation, manipulation, (motion, smoothing)
•  Conversion of 3D points and surfaces to 3D images and reverse
•  Iso-surface creation
•  3D points manipulation
•  Creation of realistic Boundary Element Models
•  Advanced 3D Drawing tool (patent filed), surface fitting

Visualisation

•  Fused and overlaid scans
•  Multiple slices, surface rendering, maximum intensity projection
•  Interactive clustering
•  Time courses, histograms, (image) profiles
•  Annotated points (dipoles, electrodes, markers, local image maxima)
•  Surfaces
•  3D-Delineations