Skip to content

FSL

FMRIB Software Library

Homepage Version(s): 6.0.5

FSL requires an environment module

In order to use FSL, you must first load the appropriate environment module: 

module load fsl

FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data.

Most of the FSL tools can be run from both the command line and as GUIs ("point-and-click" graphical user interfaces).

Using FSL on RCC Resources#

To use FSL, use the following

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
module load fsl

## Next, you need to set up your FSL environment

source $FSLDIR/etc/fslconf/fsl.sh

## Upon loading this module, all typical FSL commands will be available as shown in the docs
## Examples (see the FSL official documentation for detailed instructions)

fslmaths raw_highte.nii.gz -bptf 50 -1 filtered_highte.nii.gz
fslmaths raw_lowte.nii.gz -bptf 50 -1 filtered_lowte.nii.gz

fabber --help

feat
feat_gui

...

Upon loading this module, all the FSL programs will become available to you from the command-line.