Installed Software Packages

The following software packages are installed on the Macinstosh Computers in the ALBMC Data Analysis Room

You can bring up this page on those computers by typing 'help' on the command line in Terminal or X11

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
fMRI Lab Tools written by Mark Cohen (updated 3/7/04)
- Utilities for image processing and quality control
- 3T MRI lab How to notes
- Ana3to4d, gen2bshort, Genesis2Analyze, dcm2img, Analyze2Genesis
- EvalMasks,imconvert,Outlier,Averager,EQ,EditAnalyzeHeader,ImageInfo,SmallTime,P2P
- Launch X11 or Terminal and type the command
FMRISTAT (9/27/03)
- fMRI statistical analysis package
- FMRISTAT Home Page
- Launch matlab and type the desired command on the matlab command line
FSL 3.1
- Image analysis package
- FSL Home Page
- FSL tools
- Launch X11 and type the command (e.g., 'Bet_gui')
Gimp 1.2.4-1
- Freeware 2D image manipulation package (like Photoshop)
- Gimp Home Page
- Gimp User Manual
- 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
- IDL Virtual Machine Home Page
- 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'
LONI Debabeler
- File format converter
- LONI Debabeler Home Page
- 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 6.5.1
- Matrix manipulation and display program used by SPM
- MathWorks 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
- xmedcon documentation
- 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 September 2, 2004