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FSL is a comprensive set of tools for working with MR, fMRI and DTI data.

The GUI gives easy access to the commonly used tools: BET, SUSAN, FAST, FLIRT, FEAT, MELODIC, FDT, POSSUM and FSLView.
Don't know where to start? Have a look at Nia Goulden's quick start guide for fMRI analysis using FEAT.


FSLUTILS is a set of handy command line tools. Highlights:

  • fslchfiletype converts images between Analyse and various versions of NifTI.
  • fslhd dumps out every field in a NifTI header. This is useful when troubleshooting.
  • fslinfo returns a short summary of the dimensions of a NifTI file.
  • fslmaths a full toolbox in itself. Has everything from addition and subtraction to statistic conversions.
  • fslmeants Average a time series. Input is a 4D image and either a 3D ROI or a spatial coordinate.
  • fslmerge Concatenate 3D volumes into a 4D time series or 2D slices into a 3D volume.
  • fslsplitSplit a 4D time series into a collection of 3D volumes.
  • fslstats Produces summary statistics for an input 3D or 4D image. Useful for sanity checking images and various conversion options.

Sometimes DICOM images come through NifTI conversion flipped around or otherwise skewed. These two orientation utilities that may be just what you need to rescue your data.

  • fslreorient2std
  • fslorient

Large Jobs[edit]

FSL is installed on Odin. If you have a very large job and a slow desktop computer, it may be significantly faster to run your job overnight on Odin. See Andrew