MRI Analysis Software

UPDATE: Most of the programs below can be easily installed for Ubuntu or Debian Linux OS at Neurodebian repository at:

For FSL install fsl-5.0-core


Software recommended for working with MRI data:

***To connect from outside of UF, you will first need to install the Cisco anyconnect VPN server:

(do this before anything else)

The following work with Windows or Mac:

  1. Filezilla:

Use this program to transfer data from the MRI computer to your local computer. First go to File>Site Manager and a panel opens. On the lower left-hand side of the panel click on ‘New Site’, rename the site as something like ‘11Tesla Bruker MRI’. Starting on the upper right-hand side, enter (for 11 Tesla):


Protocol: SFTP – SSH File Transfer Protocol

Logon Type: Normal

User: LPerez

Password: luis11t

And then Press Connect or OK

  1. MRIcron:

This is a suite of tools/small programs for image viewing and image format conversion. The most important one we use here is called: dcm2nii which converts dicom files from the Bruker 11 T to 4D NIFTI_GZ format used in FSL and other programs.

  1. ITK-SNAP:

We use this to manuall segment the brain and draw volumetric masks over lesions or regions of interest.

  1. MATLAB 2017a:

(nota bene: for matlab, create an account on their website using your UF email and link your account to the UF account using the following number: 191877. Once the software is installed on your computer, I will send you a copy of the network license, called ‘network.lic’ to insert in the MATLAB directory and activate your copy)

The following work only on Mac or Linux:

  1. AFNI:
  2. FSL:
  3. XQuartz for Mac: (This is the command line program for Mac. If using Ubuntu on Windows 10 (see nota bene below), you have to install )

For those with Linux Machines you can use this resource for easy installation:


You can run all programs on Windows 10 if you turn on the Developer tools settings:

Search: ‘Developer’ using cortana on windows. Click ‘on’ developer mode. Then in the APP store for Windows download the latest version of Ubuntu 16.04.

To run Ubuntu, you first need to turn on XMing (see above). After the Ubuntu bash system is on, you may use as a Linux computer. To get to your actual local C drive desktop, you need to type the following:

cd /mnt/c/Users/YOURCPUNAME/Desktop

You’ll be using command line scripts a lot, so the following is a list of UNIX commands that you should keep handy: