WHAT'S NEW IN THIS RELEASE
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")