Setup

INSTRUCTIONS FOR SPM AND NETWORK ANALYSIS WORKSHOP PARTICIPANTS

Workshop participants should bring a laptop with MATLAB installed. SPM works with Windows, LINUX and Intel Mac systems. For Windows and LINUX you should have the 64-bit version installed. See the SPM8 page for more details concerning operating system requirements. During the course exercises, we will use SPM, MRIcron and xjview.

Computer and operating systems requirements

Please make certain that your computer has a minimum of 25GB of free disk space to accomodate the original and processed data. If you are attending one of the Network Analysis courses, you will need an additional 150GB to hold the processed data. Your machine should have a minimum of 4GB of RAM (8-16GB is better if you can manage it).

Instructions for installing SPM

  1. Install MATLAB 7.4 (R2007a) or later.
  2. Download and unpack the core SPM8 distribution
  3. Or, if you have a previous installation of SPM8, download and install the current SPM8 update
  4. Do not install the SPM8 files in the MATLAB directory structure. Instead, put the spm8 directory in a /applications folder if possible.
  5. Start MATLAB
  6. Add the SPM8 top-level directory to the beginning of the MATLAB search path. In doing so, use "Add Folder..." rather than "Add with Subfolder..."
  7. Save the new MATLAB search path and close the window.
  8. Type "spm" at the MATLAB prompt
  9. The SPM8 top-level dialog box should appear on the screen.

Please make certain that MATLAB is working on your laptop prior to the workshop. During the worshop we will be distributing datasets that will be used in the laboratory exercises.

If you do not have a MATLAB license for your laptop, you can contact the Mathworks directly to obtain a trial license. The process is not immediate, so be certain to submit your request at least at least 7 days before the course begins.

 

If for any reason you cannot get MATLAB and SPM8 working smoothly on your laptop, please contact us at spmbasics@neurometrika.org least 5 days before the course.

 

Instructions for installing MRIcron

  1. Download and install MRIcron.
  2. Read the MRIcron introduction.

 

Instructions for installing xjview

  1. Download and install xjview by copying the /xjview folder into the ../spm8/toolbox folder. Then start spm and xjview should appear under the toolbox menu.
  2. Read the xjview manual.

Instructions for installing Ghostscript and Ghostview

SPM writes graphic output to Postscript files that may be sent to a printer. These files can be viewed on your laptop using Ghostscript.

Instructions for installing Ghostscript and Ghostview for LINUX and Windows (the Mac OS includes a program called Preview that can display .ps files)

  1. Download and install Ghostscript and Ghostview.
  2. Read the Ghostscript documentation.
INSTRUCTIONS FOR SPM-FRESURFER COURSE PARTICIPANTS

    Instructions for installing VirtualBox

  1.  Download and install VirtualBox.

    Instructions for installing Neurodebian

  1. Download and install Neurodebian.
  2. After installing Neurodebian, use the Synaptic Package Manager to install nipype and FSL 5.0 (installing FSL also installs tcsh which is required for FreeSurfer).

 

 

     Instructions for installing and testing Freesurfer

  1. FreeSurfer system requirements
  2. FreeSurfer registrationFreeSurfer
  3. FreeSurfer download (pick the LINUX version)
  4. FreeSurfer installation
  5. FreeSurfer setup and configuration
  6. FreeSurfer installation testing
  7. Explore the FreeSurferWIKI

 

     Instructions for installing MATLAB

  1.  Download and install MATLAB.

     Instructions for installing SPM

  1. Download and unpack the core SPM8 distribution
  2. Or, if you have a previous installation of SPM8, download and install the current SPM8 update
  3. Do not install the SPM8 files in the MATLAB directory structure. Instead, put the spm8 directory in an /applications folder if possible.
  4. Start MATLAB
  5. Add the SPM8 top-level directory to the beginning of the MATLAB search path. In doing so, use "Add Folder..." rather than "Add with Subfolder..."
  6. Save the new MATLAB search path and close the window.
  7. Type "spm" at the MATLAB prompt
  8. The SPM8 top-level dialog box should appear on the screen.