The following software is used for CSPM. A star indicates further instructions below the table.
| Software | Required? | Instructions | Version |
|---|---|---|---|
| MATLAB | Yes |
| 2014b or later Toolboxes <required>: database; image processing; signal processing; statistics and machine learning; <optional> parallel processing, optimization |
| Ghostscript | For CSPM figure printing | Install latest Ghostscript open source software (http://ghostscript.com/download/gsdnld.html) | Current (depends on "export_fig" MATLAB add-on requirements) |
| MySQL | Yes |
| Latest version; as of writing, we are on version 5.6. The Workbench is significantly updated as of version 6.1. |
| Office | No - Used for saving subject information, timetrend files, MRI plots, documentation | Normal installation. | Any version since 2003. |
| CorelDraw | No - used for saving summaries of plots and MRI figures (check reg) | Normal installation (start once, get rid of splash screen) | Any recent version |
| VMware Player | No - required for Linux programs (FSL, FreeSurfer) |
| Version 6 and above |
| PuTTY | No - required for CSPM to run commands in Linux | Google PuTTY, go to the downloads page, choose the Windows installer, install with default options. | Any recent version |
| Python | No - used for utilities (bruker2nifti for starters) |
| Depends on python libraries being used |
| SAS | No - used for Repeated Measures ANOVA analysis of fMRI and physiology | Standard 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 |
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).
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
Python
MATLAB:
>> pyenv
ans =
PythonEnvironment with properties:
Version: "3.7"
Executable: "C:\Users\Paul\AppData\Local\Programs\Python\Python37\python.EXE"
Library: "C:\Users\Paul\AppData\Local\Programs\Python\Python37\python37.dll"
Home: "C:\Users\Paul\AppData\Local\Programs\Python\Python37"
Status: NotLoaded
ExecutionMode: InProcess
