UCLA Brain Mapping Center

Data Analysis Lab Software

Network Software Packages

The following software packages can be accessed through the BMC server DNS0 under "Imaging Tools" folder.

• AFNI 2.56d
  • FMRI data analysis package
  • AFNI Home Page
  • AFNI commands
  • Launch X11 and type 'afni' or other command on the command line
• AIR 5.2.5 (16 bit signed Analyze compatible)
  • Image registration package
  • AIR Home Page
  • AIR commands
  • Launch Terminal or X11 and type the command (e.g., 'alignlinear') on the command line
• FMRISTAT (9/27/03)
  • fMRI statistical analysis package
  • FMRISTAT Home Page
  • Launch matlab and type the desired command on the matlab command line
• FSL 4.1.4 and 5.0
  • Image analysis package
  • FSL Home Page
  • FSL tools
  • Launch X11 and type the command (e.g., 'Bet_gui')
• Gimp 1.2.4-1 (not installed)
  • Freeware 2D image manipulation package (like Photoshop)
  • Gimp Home Page
  • Launch X11 and type 'gimp'
• IDL Virtual Machine 6.0
  • Runs IDL .sav files compiled by holders of IDL licenses on other machines or platforms
  • To run a particular .sav file (e.g., file.save), open X11 and type 'idl -vm=file.sav'
  • To launch the virtual machine with a browser to choose a .sav fle, open X11 and type 'idl -vm'
• ImageJ 1.30
  • Image manipulation and analysis program
  • ImageJ Home Page
  • ImageJ Documentation
  • Launch X11 or Terminal and type 'ImageJ'
• Debabeler
  • File format converter
  • To run Siemens DICOM to Analyze conversion:
    • open Terminal or X11
    • cd to the directory where you want the Analyze files to be written
    • type 'SiemensToAnalyze' followed by the (path)names of the files you want converted
    • Note: Images will be written as transverse images in neurological format (i.e., the origin to the subject's left)
• Matlab
  • Matrix manipulation and display program used by SPM
  • Matlab Home Page
  • Matlab technical documentation
  • Note: licenses are restricted to the data analysis lab computers
  • Launch X11 and type 'matlab' on the command line
  • Note: special procedures are required to specify command line arguments in your matlab call (uncommon)
• MNI Brain Imaging Software Toolbox (Display, Register and Minc command line tools)
  • Image display and registration tools
  • Brain Imaging Software Toolbox Home Page
  • Display Home Page
  • Register Home Page
  • Launch X11 and type 'Display', 'Register' or the Minc command
• MultiTracer
  • Image display, editing and contouring
  • MultiTracer Home Page
  • Launch X11 or Terminal and type 'MultiTracer'
  • Note: If you are getting OutOfMemoryErrors you can launch MultiTracer with extra memory
• Octave
  • Matrix manipulation program (similar to Matlab)
  • Octave Home Page
  • Octave User Manual
  • Launch X11 and type 'octave'
• SPM2 (patched to 9/25/03)
  • Statistical image analysis package
  • SPM2 Home Page
  • To run:
    • Launch matlab
    • choose "Set Path" from Matlab's "File" menu
    • move the path for SPM2 above the path for SPM99
    • type 'spm' on the matlab command line
• SPM99 (patched to 9/25/03)
  • Statistical image analysis package
  • SPM99 Home Page
  • SPM99 manual
  • Launch matlab and type 'spm' on the matlab command line
• xmedcon-0.8.13
  • File format converter (DICOM and ECAT to Analyze, among others)
  • (X)MedCon Home Page
  • Lauch X11 and type 'xmedcon' (for GUI) or 'medcon ...' for command line
  • Note: xmedcon does not recognize Siemens mosaic format automatically but can decode it with hints

Updated February 25, 2019