FSL

## WHAT'S NEW IN THIS RELEASE

Release 4.1, June 2008
Minor release revision history here.

- FNIRT - FMRIB's Nonlinear Image Registration Tool. The first release of an accurate and yet fast nonlinear registration tool. This replaces IRTK, and is based on a similar warp field representation, but a) includes relative bias field modelling for improved accuracy and b) is very fast because of explicit computation of the cost function Hessian. FEAT, MELODIC, TBSS and FSL-VBM have all been updated to use FNIRT.
- FEAT v5.98. Various improvements, including FNIRT nonlinear registration, outlier modelling in higher-level analysis and higher-level voxelwise covariates (e.g., for structural confound modelling). A new script `feat_gm_prepare` makes it easy to process structural data for use as a higher-level voxelwise confound covariate.
- randomise v2.1. Various improvements, including improved handling of confounds, TFCE optimisation for TBSS and parallelisation over multiple computers.
- FAST v4.1 is now the default tissue-type segmentation program, and FAST v3 has been removed from FSL. Hence all programs including SIENA/SIENAX now use FAST v4.
- FIRST subcortical segmentation is now considerably faster, has improved boundary correction and now includes a cerebellum model.
- The outputting of ANALYZE files is no longer supported as the format is now strongly discouraged.

Release 4.0, August 2007

- MELODIC v3.0 - now contains multi-subject ICA, including Tensor-ICA spaceXtimeXsubjects decomposition.
- FIRST - FMRIB's Integrated Registration and Segmentation Tool. The first release of a new tool which uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
- FDT - FMRIB's Diffusion Toolbox now has Bayesian crossing-fibre modelling with automatic estimation of the number of crossing fibres.
- POSSUM - Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence.
- Standard Space Atlases - several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts.
- FSLView - in addition to the new atlases, new functionality includes 3D surface rendering and crossing-fibre diffusion direction viewing.
- FSL-VBM - an implementation of VBM-style analysis of grey matter density using FSL tools.
- TBSS v1.1 - improved registration efficiency in conjunction with the release of a new standard space FA template, the FMRIB58_FA. Also it is now possible to back-transform skeleton-space voxels into subjects' native DTI space, for example to allow the automated seeding of tractography in FDT.
- FABBER - Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
- The mechanism for running FSL under windows has changed. Instead of using Cygwin we now use VMware Player (freely available) with a Linux virtual machine inside it.
- FAST4 - a beta release of a new version of the FAST generic segmentation tool.
- Randomise v2.0 permutation testing - new features including: automatically correctly dealing with general contrasts and confounds, f-tests, TFCE (threshold-free cluster enhancement, a new method for cluster-based statistics).
- Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE). For example, FEAT, MELODIC, TBSS, BEDPOST (FDT), POSSUM and FSL-VBM can automatically parallelise their processing to reduce total analysis time.
- New standard space templates. We have moved to a better version of the MNI152 standard-space image. This is based on the same dataset that was used to create the avg152T1 but using nonlinear registration instead of linear (many thanks to Andrew Janke and MNI for this). MNI152_T1_2mm is the new default standard image, also available at 1mm and 0.5mm. MNI152lin_T1_2mm is what we are calling the old standard image, based on linear registration.
- FEAT - v5.90, various miscellaneous updates including partial integration of the new atlases into Featquery.
- BET - old C code now removed and replaced with equivalent "bet2" C++ program; new wrapper script "bet" which adds various functionality such as improved eye and neck removal.
- FSLUTILS: all C++ utils ending with "++" now have had the "++" stripped off, as all the old C code with a similar name has been removed. Also, all programs starting with "avw" are now renamed to start with "fsl", e.g. "fslmaths". A script "avw2fsl" has been provided to help convert users' shell and TCL scripts to use the new command names.
- NIFTI i/o updated to use the sourceforge library.
- Warp field inversion is now possible with "invwarp".
- Removed FSL dependency on Tix, Gnuplot and ImageMagick; any generic recent TCL/TK can now be used for the scripts and GUIs.

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

- 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")

FSL 4.1 minor release revision history

- 4.1.0 12/8/08 First release
- 4.1.1 15/10/08 Minor bug fix release
  There are are a number of minor bug fixes in FEAT and FDT.
  FNIRT should now be able to locate cnf files more robustly.
- 4.1.2 02/12/08 Minor bug fix release
  There are are a number of minor bug fixes in FEAT, FDT, BET and FNIRT.
- 4.1.3 23/04/09 Minor bug fix release
  All binaries now have improved capabilities in handling large ( >4Gb ) image files.
  An issue of randomise generating overly-conservative p-values for f-stats/partial model effects has been fixed.
  ProbtrackX has a fix to termination mask usage.
  A bug has been fixed in FIRST vertex-wise stats.
  An atlas of the Cerebellum has been added to fslview ( courtesy of Joern Diedrichsen and Narender Ramnani ).
  The Juelich cyto- and myelo-architectonic atlas has been upgraded ( courtesy of Simon Eickhoff ).
  The run_mesh_utils binary is now included in the distribution.
- 4.1.4 22/05/09 Minor bug fix and FIRST upgrade release
  FIRST has a number of changes - it is recommended to rerun previous analyses with this version.
  An issue with abnormal termination of FLAMEO on 32-bit systems has been resolved.
  There are minor bug fixes to FEAT and FSLView.
  The FAST gui now has an additional bias-field option.
  The tbss_sym script has been added to TBSS.
  There are some small documentation changes.
- 4.1.5 22/01/10 Minor bug fix release
  An issue with Randomise "pausing" has been fixed.
  The Posterior Insula has been added to the Juelich cyto-architectonic atlas, courtesy of Simon Eickhoff.
  There are some improvements to the bedpostx monitor script.
  Large speedup for invwarp by automatically adjusting the useful FOV internally (no cropping of the original images needed).
- 4.1.6 01/07/10 Minor bug fix release
  An inconsistency with the -s input for fast4 has been fixed.
  A bug has been fixed for the randfib option in probtrackx.
  There is a new, easy to use tool for reorienting images to match the standard template image orientation (fslreorient2std).
  A bug has been fixed in flirt when very high-resolution images are used together with -init matrices.
  The input-parsing of feat_model is much improved, courtesy of Jeremy Reynolds.
- 4.1.7 14/01/11 Minor bug fix release
  A problem with TFCE in fslmaths has been fixed.
  There are some improvements to error detection in randomise.
  MELODIC now has an option to use a user-defined seed.
  There are a number of minor fixes to FEAT.
  fslmerge now attempts to detect orientation problems during a temporal merge.
- 4.1.8 15/05/11 Minor bug fix release
  There have been some improvements to the initialisation routines in xfibres.
  An issue with the -e option in randomise has been resolved - please see the randomise documentation for more details.
  A bug in the --peakdist option in cluster has been fixed.
- 4.1.9 17/10/11 Bug fix release
  A large number of minor patches, corrections and compatibility fixes.
  Slice-timing correction in FEAT should be much more accurate.