Where can I find help, tutorials or papers about FSL?

Documentation for all FSL tools can be found via the FSL wiki: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/

A tutorial-based set of lecture slides and practicals can be found at https://fsl.fmrib.ox.ac.uk/fslcourse/ and is related to the content of the FSL course which is held once or twice each year - see the course website for details on upcoming/recent courses.

Further help can also be obtained via the public FSL email list. Note that you must join the list in order to post questions.

Finally, detailed technical reports can be found at https://www.fmrib.ox.ac.uk/analysis/techrep/ and a full list of conference and journal papers produced by the FMRIB Analysis Group can be found at https://www.fmrib.ox.ac.uk/analysis/fmribindex/.

How do I best report problems to the FSL email list?

In order to understand and analyse problems please provide the following pieces of information:

What image format does FSL need?

FSL programs primarily expect to read NIFTI-1/NIfTI-2 format images. These files can be read and written in compressed (gzip format) or uncompressed form. To convert between these different formats, use the fslchfiletype utility or the environment variable FSLOUTPUTTYPE. These are described more fully in the nifti1 page.

An image can be 2D or 3D or 4D (multiple time points).

FSL programs for FMRI analysis use single 4D NIFTI images, not lots of 3D images (such as SPM does).

You will need some other program to convert between formats (e.g. DICOM). We recommend using dcm2niix for DICOM to NIfTI conversion.

How do I convert between 3D and 4D NIFTI images?

In order to convert between multiple 3D and single 4D images, use the following programs (found in $FSLDIR/bin):

3D -> 4D

In general, due to the multiple file formats, we recommend using the utility imglob for getting filenames. For example:

4D -> 3D

this program automatically chooses the output name.

How can I modify the orientation of my data?

Please look at the "Orientation-related Utilities" section of the FSLUTILS documentation page.

How do I know right from left in the images?

Look at the labels in FSLeyes. For more information about orientation, the NIfTI format and FSLeyes display, see the "Orientation-related Utilities" and "Background information on NIfTI Orientation" sections of the FSLUTILS documentation page.

How do I run the GUIs or command lines?

On most machines the GUIs can be run by:

However, under MacOSX the GUIs are run by:

On all machines, the command line versions can be run by typing the name of the program, all in lower case: e.g. flirt Note: with no arguments the command line versions return a help statement that includes usage lines and available options.

How do I get my command line to run?

Many things might be the cause of this, but the following list covers the vast majority of problems:

Why does an FSL program crash when it is trying to process a very large dataset?

Certain programs in FSL can require a large amount of memory (RAM) to run, depending on the size of the data that you are trying to analyse. For example:

The memory available to a program depends on how much physical RAM you have on your computer, what other programs are already running, and how much "virtual memory" (swap) you have configured. Swap is hard disk space that is used to act as additional memory on top of your actual memory, allowing programs larger than your physical memory to run, but much more slowly. Hence, if your program is running out of memory you should consider increasing your physical RAM and/or your swap space (the latter is cheaper but a slower solution). Your local sysadmin can easily increase swap space if you have spare hard disk space available.



FSL FAQ (last edited 13:41:01 25-11-2022 by PaulMcCarthy)