WHAT'S NEW IN THIS RELEASE
Release 3.3, April 2006
- TBSS - first
release of Tract-Based Spatial Statistics, for voxel-based
multi-subject statistics on diffusion (e.g. FA) data. TBSS uses the
IRTK nonlinear registration software, binaries of which are bundled
with this release of FSL.
- FEAT v5.6 new
features:
- Perfusion FMRI modelling/subtraction
- Contrast estimability (meanginful rank deficiency and
efficiency estimation)
- FUGUE EPI unwarping now an option in pre-stats, to be applied
simultaneously with motion correction; slice timing correction
moved to be run after both
- Motion parameters can now be automatically added as confound
EVs into the model
- New wizard for a few simple higher-level design setups
- Empty EVs are now allowed at first level (for consistent
naming across multiple subjects)
- FSLView v2.4 new features:
- Timeseries plotting of model vs. data for FEAT output
- FEAT cluster table interaction
- Various other smaller improvements, plus full compilable source code now distributed
- Featquery changes:
- % signal change calculations are now fully automated for both
complex contrasts and higher-level FEAT output
- Coordinate of max voxel also now reported in standard space mm
- Raw text file output added
- Glm: A new GUI (a stand-alone version of the FEAT design
matrix sub-GUI) for creating design matrix and contrast files, for
example for use in randomise.
- SIENA v2.4 - the
siena and sienax scripts can now pass on all relevant options to BET
and FAST. Also the text output from sienax now includes unnormalised
volume reporting as well as the head-size-normalised volumes. (Note
also that small changes in FLIRT and FAST will mean that SIENA/SIENAX
results may be very slightly different from the previous version.)
- FDR command-line program (fdr) is updated with a new definition of
valid-voxel mask generation.
Release 3.2β, September 2004
Note: the commands for setting up your environment to use FSL have
changed very slightly - see the Running section of downloading and
installing.
- FDT (FMRIB's Diffusion Toolbox) -
first release of this complete toolkit for analysis of diffusion
data, including probabilistic tractography.
- FLOBS (FMRIB's Linear
Optimal Basis Functions) - a new method for finding an optimal set of
HRF convolution basis functions, plus a Bayesian estimation method
for improving signal/noise separation using these basis functions.
- SMM (Spatial Mixture Modelling) -
a new tool for alternative hypothesis testing on statistic images
using histogram mixture modelling with spatial regularisation of the
voxel classification into activation and non-activation.
- Randomise - a
randomisation-based inference tool for nonparametric statistical
thresholding.
- BET v2 - can now estimate mesh
representations of the inner and outer skull surfaces, and outer
scalp surface, for example for use in EEG/MEG source modelling.
- NIFTI - FSL now uses
the NIFTI-1 data format by default (though can still read and write
old Analyze files). Single-file NIFTI-1 images can be read and written
already compressed, saving much disk space.
- FEAT v5.4 new
features:
- Use of FLOBS (optimised HRF basis sets).
- Fixed-effects higher-level analysis (e.g. for within-subject
cross-session analysis).
- Option to prevent cleanup of standard-space first-level stats.
- User preferences file (and network-wide preferences file)
which can set FEAT preferences for loading on startup.
- Inclusion of MELODIC data exploration at the end of Pre-stats.
- Time-series (data vs model) plotting inside Featquery.
- SIENA - can now do
voxelwise cross-subject statistical atrophy analysis. Also, there is a
small change to the partial volume estimation in FAST, causing slight
differences in volume estimates; any multi-subject analysis using
FAST/SIENAX estimated volumes must only use the previous
version or only use this new version.
- fslerrorreport is a new script which should always be run before
emailing the FSL email list with a problem concerning running programs
- the output from this will give us useful information about your
system.
Release 3.1, July 2003
- FLAME (Bayesian group stats modelling and estimation in FEAT5):
updated to give increased estimation accuracy at the MCMC stage, and
with added option for "FLAME stage 1 only" (nearly as fast as OLS and
nearly as accurate as full FLAME).
- Beta-release of FSL for WindowsXP using Cygwin.
- Beta-release of FSLView interactive 3D/4D viewer (currently compiled
for Linux/MacosX/Windows i.e. not yet IRIX/SunOS).
- Various minor additions (such as progress viewer for FEAT) and bug-fixes.
Release 3.0, October 2002
- FEAT v5:
- Bayesian multi-subject FMRI analysis: General GLM for
higher-level analysis (e.g. analysis across sessions or across
subjects; paired t-tests, three-level groupings etc): FLAME (FMRIB's
Local Analysis of Mixed Effects). FLAME uses very sophisticated
methods for modelling and estimating the random-effects component of
the measured inter-session mixed-effects variance, using MCMC to get
an accurate estimation of the true random-effects variance and degrees
of freedom at each voxel.
- Slice timing correction
- Basis function HRF convolutions
- Pre-threshold masking
- Contrast masking after thresholding
- Optionally registration can use two structural images as well as
standard space image.
- Peristimulus timing plots in the web report.
- Featquery - a program which allows you to interrogate FEAT results by
defining a mask or co-ordinates (in standard-space, highres-space
or lowres-space) and get mean stats values and time-series.
- Although IRVA (semi-model-free analysis) is still bundled with
FSL, it is no longer an option within FEAT. This is because this kind
of analysis is effectively covered as a subset of the functionality of
FIR basis function analysis in FEAT.
- MELODIC v2:
- Probabilistic ICA (PICA) for FMRI. By adding a Gaussian noise
model to the ICA model, and automatically estimating the
dimensionality (the number of non-Gaussian components), it is now
possible to create meaningful Z-statistic maps for each spatial
component, allowing inference ("thresholding").
- Inference on the Z-statistic images is carried out with a
Gaussian/Gamma mixture model (fitted using EM), fitting central noise
and activation classes; thus alternative hypothesis testing is used.
- Interoperation
with FreeSurfer - it is now very easy to display FEAT results onto
FreeSurfer-generated inflated or flattened surfaces, and also easy to
carry out group FEAT analysis in standard-spherical-surface space
instead of 3D standard space.
- Interoperation with
AFNI - AFNI can now easily read FSL (particularly FEAT) output for
easy visualisation.
- SIENA v2: increased accuracy by forcing all steps to be symmetric;
added masking functionality including standard-space-based Z limits.
- FLIRT&MCFLIRT; now run on single-slice (or few-slice) data; the
flirt -applyxfm option now allows the processing of 4D data; new GUIs
- ApplyXFM, ConcatXFM.
- BET: new command-line options for surface initialisation; "bet"
now runs on binarised and on 2D images; the "betpremask" script uses
FLIRT registration to do standard-space masking instead of running
"bet"; bet now works on 4D images in two possible ways (the "betfunc"
script is suited to motion-corrected FMRI data, applying
over-inclusive masking, whilst just running "bet" on 4D data estimates
the brain mask from the first image and applies this to the rest);
Releases 2.0 - e, internal development versions
Release 1.3 for Mac OS X, November 2001
Release 1.3, June 2001:
- New: MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data.
- New: FAST - Brain segmentation (into different tissue types) and bias
field correction.
- New: FUGUE - Unwarps geometric distortion in EPI images using
B0 field maps.
- New: SIENA - Structural brain change analysis, for estimating brain
atrophy.
- FEAT 4.03: new features include F-tests and improved organisation
of GLM-setup GUI.
- FLIRT: new features include image masking/weighting, different
output interpolations, and allowing 2D registration.
Release 1.2a, May 2001 (not an FSL release but the version bundled
with MEDx 3.40):
- FEAT 4.02: new features include F-tests and improved organisation
of GLM-setup GUI.
Release 1.2, December 2000:
- All GUIs can now run standalone - i.e., nothing in FSL needs
MEDx in order to run.
- FSL now includes MCFLIRT motion correction, which is more
accurate, and faster, than the other tested MC methods. FEAT uses
MCFLIRT only.
- FILM (the GLM method inside FEAT) now uses general
least-squares, prewhitening the data before the final fitting. This
gives more efficient activation estimation than the other methods
tested, particularly for dense single-event experiments. It includes
autocorrelation correction, using smoothing of autocorrelation
coefficients and nonlinear spatial filtering to achieve robust
estimation.
- A new GUI "fsl" which calls the other main FSL tools.
- The "model-free ANOVA" method has been renamed "IRVA"
(Inter-Repetition Variance Analysis) to avoid later confusion with ICA
truly model-free analysis (to be released shortly).
Release 1.1, August 2000:
- FEAT (FMRI analysis) will now use FLIRT (registration) to
automatically register your FMRI data to a high-resolution structural
and/or standard image for you, without having to use the FLIRT GUI
separately.
- FEAT can now run group statistics (fixed-effects and random-effects)
across groups of FEAT directories, either in a single long FEAT run
(consisting of multiple first-level analyses followed by group-stats)
or on previously created FEAT directories.
- You can now explicitly demand that certain EVs in FEAT be
orthogonalised with respect to other EVs in the design matrix.
- FSL now works with both the latest MEDx release (3.30) and the
previous version (3.20).
Release 1.0 (beta), June 2000. First ever release, containing:
- BET
- SUSAN
- FLIRT
- FEAT
- IRVA (then referred to as "Model-free ANOVA")