FSLeyes

FSLeyes#

Introduction#

FSLeyes, which is part of the FMRIB Software Library (FSL), is an image viewer for 3D and 4D neuroimages. It is a commonly used package in the field of neuroimaging, and our lab has several plugins that integrate with FSLeyes.

Installation #

The FSLeyes documentation provides two different install options:

  1. Install as part of FSL

  2. Install through conda-forge

Requirements when running from OSX: XQuartz

Install FSLeyes from conda-forge (this has to be done in a virtual environment) on the remote host (rosenberg or joplin):

conda create --name <YOUR_ENV>
conda activate <YOUR_ENV>
conda install -c conda-forge fsleyes

Running Remotely#

To run FSLeyes remotely, please see the documentation here.

After installing, do an ssh for X forwarding:

ssh -X username@remotehost
conda activate <YOUR_ENV>
fsleyes

If you have an XQuartz error follow the instructions here.

Plugins#

We have several different projects with FSLeyes-integrated plugins: