Anatomical Processing Script: fsl_anat (BETA version)

This tool provides a general pipeline for processing anatomical images (e.g. T1-weighted scans).

Most of the pipeline involves standard use of FSL tools, but the bias-field correction has been substantially improved, especially for strong bias-fields typical of multi-coil arrays and high-field scanners.

The stages in the pipeline (in order) are:

The overall run-time is heavily dependent on the resolution of the image but anything between 30 and 90 minutes would be typical.


Various stages in the pipeline can be turned off. Currently not all combinations have been tested and so users are advised to only turn off the first few or last couple of stages currently.

Usage: fsl_anat [options] -i <structural image>
       fsl_anat [options] -d <existing anat directory>

Arguments (You may specify one or more of):
  -i <strucural image>         filename of input image (for one image only)
  -d <anat dir>                directory name for existing .anat directory where this script will be run in place
  -o <output directory>        basename of directory for output (default is input image basename followed by .anat)
  --clobber                    if .anat directory exist (as specified by -o or default from -i) then delete it and make a new one
  --weakbias                   used for images with little and/or smooth bias fields
  --noreorient                 turn off step that does reorientation 2 standard (fslreorient2std)
  --nocrop                     turn off step that does automated cropping (robustfov)
  --nobias                     turn off steps that do bias field correction (via FAST)
  --noreg                      turn off steps that do registration to standard (FLIRT and FNIRT)
  --nononlinreg                turn off step that does non-linear registration (FNIRT)
  --noseg                      turn off step that does tissue-type segmentation (FAST)
  --nosubcortseg               turn off step that does sub-cortical segmentation (FIRST)
  -s <value>                   specify the value for bias field smoothing (the -l option in FAST)
  -t <type>                    specify the type of image (choose one of T1 T2 PD - default is T1)
  --nosearch                   specify that linear registration uses the -nosearch option (FLIRT)
  --betfparam                  specify f parameter for BET (only used if not running non-linear reg and also wanting brain extraction done)
  --nocleanup                  do not remove intermediate files

By default:

Using the -d option the script can be run again (with a subset of stages) to update an existing result.


This section describes the main output files - it is not a complete list, but highlights the most important outputs.


The output directory will end with .anat and by default will have the same basename as the input image (and be in the same directory). If the -o option is used the directory name will use the specified name, followed by .anat

Original image

The specified input image is copied into the output directory and named T1, T2 or PD, depending on the setting of the -t option (default is T1).

Reorientation and Cropping

If run, the original image (we shall call it T1 from here on in as an example), will be replaced by the reoriented and/or cropped version. The original versions are saved as files: T1_orig and T1_fullfov.

In addition, transformation files are provided to allow images to be moved between spaces: i.e. T1_orig2std.mat and T1_nonroi2roi.mat and their inverses and combinations.


The bias-corrected version of the image is called T1_biascorr.

Registration and Brain-Extraction

The registration (to standard space) produces the following images that are in MNI space with a 2mm resolution:

The brain-extraction produces:


Tissue-type segmentation (done with FAST) produces:

Subcortical segmentation (done with FIRST) produces:


fsl_anat (last edited 19:57:57 26-04-2013 by ThomasNichols)