Analysis Programs

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Program List

In alphabetical order:

Analysis of Functional NeuroImages (AFNI)

BrainVoyager

FMRIB Software Library (FSL)

Statistical Parametric Mapping (SPM)

PyMVPA

See project's homepage for the information on installation and use. On DBIC's AFS-capable systems, PyMVPA is available under /afs, adjust your PYTHONPATH accordingly.

FSL (FMRIB)

  • To run:
    $ fsl & 
  • Environmental variables:
    The FSL_DIR environmental variable contains the install dir.
    Our current default output file format is ANALYZE. This can be changed with the FSLOUTPUTTYPE environment variable.
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/fsl
  • Installed Version: 3.3.10
  • Availability: x86_64, x86, and SPARC
  • Application website.
  • Download this application.

mri3d

  • To run:
     multitracer.sh & 
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/mri3dx
  • Installed Version: 31.27
  • Availability: x86 and x86_64
  • Application website .
  • Notes: Recent versions of Linux may not be supported by this software.

MultiTracer

  • To run:
     multitracer.sh & 
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/multitracer
  • Installed Version: 1.0
  • Availability: All (Java)
  • Application website.

MRIcro

  • To run:
     startmricro & 
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/mricro
  • Installed Version: 1.39 build 4
  • Availability: x86_64 and x86
  • Application website.

MRIcron

  • To run:
     mricron & 
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/mricron
  • Installed Version: Beta 1
  • Availability: x86_64 and x86 (Linux)
  • Application website. </ul>

    CARET

  • To run:
    $ caret & 
  • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/caret
  • Environmental variables:
    The CARET_HOME environmental variable contains the install dir.
  • Installed Version: 5.5
  • Availability: x86_64, x86, SPARC
  • Application <a href="http://brainmap.wustl.edu/caret/">website</a>. </ul>

    SPM (UCL)

    • To run:
       
      $ matlab
      >> spm fmri             
      
    • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/spm
    • Installed Version: 99, 2, and 5
    • Availability: x86_64, x86, SPARC
    • Application website.
    • The SPM2 Updates readme.
    • The SPM5 Updates readme.

    AIR (UCLA)

    • To run:
      $ align_warp 
    • Environmental variables:
      The AIR_HOME environmental variable contains the install dir.
    • Application Directory: /afs/dbic.dartmouth.edu/usr/pkg/AIR
    • Installed Version: 5.2.5
    • Availability: x86_64, x86, SPARC
    • Application website.
    • Notes:
      There are four GUIs (align.tcl, align_warp.tcl, reslice.tcl, reslice_warp.tcl) available. These are written in TCL/TK and should be in the standard PATH. Execute the application name to run.
    == Scripting ==