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