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The following software is used for CSPM. A star indicates further instructions below the table.

SoftwareRequired?InstructionsVersion
MATLABYes
  • Install with default options
  • Set startup file to run for all users (star) (see details below)

2014b or later

Toolboxes <required>: database; image processing; signal processing; statistics and machine learning; <optional> parallel processing, optimization

GhostscriptFor CSPM figure printingInstall latest Ghostscript open source software (http://ghostscript.com/download/gsdnld.html)Current (depends on "export_fig" MATLAB add-on requirements)
MySQLYes
  • Uninstall any previous versions; you may want to delete the data (backup the database before), which is in C:\ProgramData\MySQL. The folder is hidden, so type in the address; delete the MySQL folder.
  • Google "mysql community server"; download and run "MySQL Installer"; choose the large file (~270MB in 2014) as this is more reliable than the other. (green star) (see details below)
  • Run the downloaded installer; choose custom installation, and select the 64-bit MySQL Server, the Workbench, and the Connector/J. § (see details below)
  • Choose the default options; write down the password for the "root" account (root is a common term for Administrator account); there is no need to create user accounts.

Latest version; as of writing, we are on version 5.6.

The Workbench is significantly updated as of version 6.1.

OfficeNo - Used for saving subject information, timetrend files, MRI plots, documentationNormal installation.Any version since 2003.
CorelDrawNo - used for saving summaries of plots and MRI figures (check reg)Normal installation (start once, get rid of splash screen)Any recent version
VMware PlayerNo - required for Linux programs (FSL, FreeSurfer)
  • Google VMware Player; you will probably land on the VMware downloads page, which has VMware Player right at the botttom (link on right of page). Download- you probably need to register (but it's free).
  • Normal installation - take defaults.
Version 6 and above
PuTTYNo - required for CSPM to run commands in LinuxGoogle PuTTY, go to the downloads page, choose the Windows installer, install with default options.Any recent version
PythonNo - used for utilities (bruker2nifti for starters)
  • Check you current installation: in MATLAB, type >> pyenv. This will return if installed on the computer, and it will show the version
  • In install or update, go to phython.org, download and install the latest version (see below)
Depends on python libraries being used
SASNo - used for Repeated Measures ANOVA analysis of fMRI and physiologyStandard installation.Any version.
MRIConvert

No - alternative DICOM converter, may be useful

* dcm2nii that comes with mricron may be better

Install under folder C:\Program FIles (x86)\MRIConvert (win32 version)

Google - as of 2020-07 https://lcni.uoregon.edu/downloads/mriconvert/

Any version

(star) MATLAB startup file: when started, MATLAB will run a script if it finds a file called "startup.m". This is useful for automatically starting SPM, including various versions. In ~2012 and earlier versions, this script was located in C:\Program Files\MATLAB\R2012a\toolbox\local. However, in later versions, this file defaults to users' local folders (in Documents\MATLAB). The advantage of this location is that when MATLAB is upgraded, the startup file does not need to be copied. This option is best for computers with mostly one person logging on.

If more than on person uses the computer, the startup file would need to be copied to each user's documents\MATLAB folder, so it may be simpler to place the file in the original, release-specific subfolder. To have MATLAB run the same script for all users:

    • With Windows Explorer, navigate to C:\Program Files\MATLAB\[R2012a]\toolbox\local (R2012a will vary according to the version installed)
    • Set the permissions to read/write: Right-click over the folder name, Properties, Security tab, Edit, select "Users", check "Full control", OK, OK.
    • Copy the provided startup.m file into this folder
    • When you start MATLAB, it will run the script (startup.m is the script).

(green star) MySQL Download quick link: after clicking "Download," it seems like you have to sign up, but there is a half-hidden like to avoid this:

§ MySQL custom setup



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