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How to Process MRI Images:
- Beginner's Guide to Command Line Interface
- More about the Command Line Interface
- NITRC, a source for neuroimaging software and data.
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Before you begin
- Computer setup and Applications
- Preprocessing and processing images
- MRI File Formats
- Download example test-retest multi-modal dataset
- Alternative option for test-retest MRI data
- More public datasets
- Convert DICOM to NIfTI
- BIDS and dcm2bids: Structuring your data sets
- Correct intensity nonuniformities (bias field)
- Resample images to isotropic voxel size 1
- Brain Extraction and Tissue Segmentation
- Hippocampus Segmentation
Generally neuroimaging computing is done on Linux or macOS. You may need to be logged in as root to install many of these programs, depending on the permissions of the directory on which you are installing. The following are specifics about operating systems I currently use to run neuroimaging analyses:
Version Notes
- macOS (10.12+)
- You should install XCode first before beginning any of these other tasks. The version of XCode will vary, depending on your OS version XCode
- In order to have access to root user you have to directly enable the option, for instructions refer to this page here. If you are on a university or company managed computer, it's a good idea to talk with your IT administrator before installing any software (if you have administrator access).
- Ubuntu 18.04.1 (Bionic Beaver)
- Windows 10 with the Windows Subsystem for Linux activated and Ubuntu installed. If you are using Windows it may be easier to log in as the Administrator for all of these downloads. If you are using a managed computer, you will likely need your IT administrator to install any software.
Attention Windows Users
Some imaging programs (MANGO, dcm2nii, mricron, and some functions of ANTs) can be installed onto Windows easily but you will quickly find barriers between programs. The neuroimaging community likes to run things on Linux or macOS (although SPM runs well on Windows so many people who do only fMRI research use Windows). If you are interested in having these programs on your own computer I suggest a free installation of Linux. Ubuntu, Mint, Debian, CentOS, and others work well. Ubuntu is quite easy to use and learn. If you aren't fully committed to using just Linux you can run it in a Virtual Machine or partition your drive to dual boot, which allows you to run Linux or Windows upon restarting your computer each time. NeuroDebian is a VM that can be installed and run without too much difficulty. I won't reproduce the installation instructions here.
Another option mentioned previously is with Windows 10 and the Windows Subsystem for Linux. Follow those instructions to get this useful tool installed. Once you enable the WSL, you can easily install your Linux distribution of choice. There are some limitations to the WSL relative to a "pure" installation of Linux but it gives access to a number of the tools previously unusable in Windows. Windows Subsystem for Linux Documentation