The following software is used for CSPM. An asterisk (*) A star indicates further instructions below the table.
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Software | Required? | Instructions | Version |
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MATLAB | Yes |
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2021a or later Toolboxes <required>: |
database |
; image processing |
; signal processing; statistics and machine learning; <optional> parallel processing, optimization Optional (required for some functions): see installation details. | |||
MRICroGL | No, but a useful backup conversion tool | NITRC (or google it); the download is a zipped file. Unzip; copy the “mricrogl” folder to “C:\Program Files\”; right-click over “MRIcroGL.exe” and add to taskbar | Worth keeping up to date to ensure compatibility with lastest DICOM files; also there is a fair amount of development, so bug fixes and new features |
MRIcronN | Semi-obsolete as Chris Rorden wants to only develop MRICroGL; but still a great nifti viewer | Same instructions as MRICroGL | |
Ghostscript | Helpful 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/MariaDB | Yes (but usually provided by IT) |
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| 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 |
- Go to your Google account, select the Drive App, and install on your computer. Sign in to your account.
- Get the link from Paul to the matlab folder; open this link, and "Add to Drive" (top-right).
- Google drive will synchronize everything on your Google drive with the folder "Google Drive" on your computer, which will show up under Favorites. (The first time matlab will take 3-5 hours to sync.)
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. |
* 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), which is a problem if more than on person uses the computer. To have MATLAB run the same script for all users (recommended):
- 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 should run the script (startup.m is the script).
MRIConvert | Not recommended; used to work ~2015 * 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 |
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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:
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