WHAT'S NEW IN THIS RELEASE
Release 6.0, October 2018
Minor release revision history here.
- This version has major changes to the lower-level image and matrix libraries to improve capabilities and performance for larger data sets.
eddyqc performs automated dMRI data assessment, both at the single subject and group levels
FSLeyes: Now includes Jupyter notebook integration, maximum-intensity projection and a new plugin architecture.
- FSLpy includes wrappers for certain FSL commands.
- The HCP1065 standard space DTI templates have been added
- fsl_ents is a tool for extracting component timeseries from an ICA directory ( e.g using the output from FIX )
- Tools are now NIFTI-2 capable, although this should currently be regarded as beta-functionality.
- This also includes the latest versions of tools introduced since the last major update:
MIST: a tool for multi-model subcortical segmentation.
MSM: a tool for cortical surface registration.
BIANCA: A tool for automatic ( trained ) segmentation of white-matter hyperintensities.
Release 5.0, September 2012-2018
Minor release revision history here.
- New live Wiki-based documentation (you're looking at it!)
Dual Regression - maps a set of group-ICA spatial maps back into individual subjects' datasets
BASIL - a new suite of tools for the quantification of resting perfusion from Arterial Spin Labeling MRI, including correction for variable bolus arrival time, macro vascular contamination and the effects of partial voluming.
BBR - a new option for EPI to structural registration, which is an implementation of Doug Greve's Boundary-Based-Registration method that includes built-in fieldmap-based distortion correction. This is now the default option for all FMRI to structural registrations as it has been found to be substantially more accurate, and is now built into FEAT and MELODIC registration.
PNM - Physiological Noise Model is a tool for correcting physiological noise, based on cardiac and respiratory recordings (typically, but not restricted to, pulse-ox and bellows). It provides the standard RETROICOR-style regressors as well as additional ones including interactions (cardiac * respiratory), RVT, heart rate. This is strongly recommended to be used in any FMRI studies focussing on the brainstem, spinal cord, or other structures in the inferior part of the brain.
Atlases - Oxford-GSK-Imanova structural and connectivity striatal atlases - two main atlases provided that sub-divide the striatum based on (i) the white matter connectivity to major functional regions of the cortex and; (ii) a structural atlas derived from literature-based rules that subdivides striatum into caudate, putamen and ventral striatum.
FIRST - a new vertex analysis method, based on projection to the average surface normal, that provides (i) a general GLM setup, including arbitrary contrasts; (ii) input images for randomise (not surfaces); and (iii) a new selection of multiple-comparison methods to be employed for vertex analysis. In addition, the old vertex analysis method, with surfaces, remains available.
Fieldmaps - fsl_prepare_fieldmap is a tool designed to make the initial processing of fieldmaps easier (designed for only Siemens scanners currently). It creates the necessary inputs (rad/s map and magnitude) for FEAT processing.
Randomise - Lesion masking - a new script, setup_masks, is supplied to assist in using lesion masks (user-supplied) in randomise to exclude (inconsistently located) lesions from group studies.
Lesion Filling - a new tool for taking structural images and filling lesion areas (specified by user-defined masks, e.g., drawn by hand) in order to improve segmentation and registration performance.
SIENA - a separate ventricle-based analysis is now possible
Probtrackx2 - A new version of the probabilistic tracking tool that includes many more options such as: handling surfaces (from Caret, FreeSurfer and FIRST), mixtures of images and surfaces, matrices output, and more...
- Various updates to the FDT GUI. It allows the user to set all the available command-line options
BedpostX - A new model for estimating fibre orientations using multi-shell data is available. Also new options for modelling different noise distributions.
Qboot - A tool for estimating fibre orientations non-parametrically using ODFs (orientation distribution functions). Uncertainty is estimated using residual bootstrap.
Tools for processing surface files, such as surf2volume, surf2surf, surf_proj
fsl_anat (BETA version) - Anatomical Processing Script (BETA version) - a flexible new tool that combines the existing features of brain extraction (BET+FNIRT-based masking), registration (FLIRT + FNIRT), tissue-type segmentation (FAST), subcortical segmentation (FIRST), with substantially enhanced bias-field correction and automatic reorientation and cropping.
topup (BETA version) - A tool for estimating and correcting susceptibility induced distortions
eddy (BETA version) - An advanced, highly tailored and accurate tool for correcting eddy-current-distortions
A large array of minor improvements and additions to tools (e.g. massive speedup to invwarp, fill holes in fslmaths, spline interpolation in flirt, DVARS option in fsl_motion_outliers, ...)
Release 4.1, June 2008
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.
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:
- IRVA (then referred to as "Model-free ANOVA")
FSL 5.0 minor release revision history
- Fixed critical scripting issues with FEAT
- Fixed post-hoc output timecourses in MELODIC
- Minor fixes to a small number of source files
- Numerous minor bug fixes
- Added Subthalamic Nucleus Atlas, courtesy of Birte Forstmann
- fsl_sub patch
- FSLview patch for HCP
- Harvard-Oxford subcortical atlas fix
- Minor bug fixes and feature enhancements
- Timeseries masking fixed in fslstats
- Precision fix in smoothest
- Build environment variables for OSX Mountain Lion
- Documentation updated to latest online wiki
- improvements to robustfov
- Fixed an issue with MELODIC Group ICA introduced in 5.0.3
- Changes for HCP pipeline compliance
- Updates to some atlas definitions
- Bedpostx is now CUDA capable for GPU-equipped clusters, please see the wiki for information on usage and configuration.
- Bedpostx now has a gradient non-linearity option.
- Probtrackx2 can now output an ROIxROI network matrix.
- A bug in concat mode in the FSL 5.0.4 version of MELODIC has been fixed, it is recommended to re-run any temporal-concatenation analyses run with that version.
- An issue with some MELODIC analyses not converging has been resolved.
- Bug fixed for multishell qboot.
- An error with voxelwise regressors in lower-level FEAT introduced in FSL 5.0.5 has been fixed. We would strongly recommend re-running any lower-level FEAT analysis that used voxelwise regressors ( e.g. PNM ) generated with FSL 5.0.5
- An issue with POSSUM has been resolved.
- FSL enviroment scripts have been updated for OSX Mavericks.
- The ASL GUI has been updated.
- The analysis options for lower-level FEAT have been simplified to match changes in the processing pipeline
- FSL can now be compiled on the latest version of OSX ( using LLVM )
- Improvements have been made to the accuracy of POSSUM for a range of smaller voxel sizes and large motions.
- oxford_asl: Corrected the values for inversion efficiency for pASL and cASL data, correct assignment of default BAT value for cASL (now matches with usage).
- Connectivity-based parcellation atlases have been added, courtesy of Rogier B. Mars.
- The highpass temporal filter in fslmaths now removes the mean component
- a bug in the header information of topup output files has been fixed
- FEAT has improved handling of non-fatal error conditions
- An error in the asl_calib script has been fixed
- An issue with missing images in the VIENA report has been resolved.
- All FSL scripts now internally set their locale to C
- A potential race condition with multiple calls to maskdyads or slices has been corrected.
- FDR now saves adjusted values as 1-p if the input is 1-p.
- Verbena: Initial release of model-based analysis of perfusion from DSC-MRI based on the vascular model, including the option to separately estimate the arterial/macrovascular component.
- asl_calib bug fix for default T2 values
- oxford_asl - tidy up of usage, option for voxelwise calibration and improved compliance with consensus ‘white’ paper quantification approach, option to specify the noise prior (particularly for single TI data)
- asl_file - includes the option for surround subtraction
- quasil - fix to dispersion option;
- randomise has much improved handling of voxelwise regressors
- fsl_anat now has separate options for weak and strong bias field correction, with a change in the default to weak bias
- dtifit has now the option for correcting for gradient non-linearities unhidden
- eddy_correct has an option to choose the type of interpolation used (trilinear, spline)
- select_dwi_vols allows quick extraction of a certain b-shell from DWI data
bedpostx has a new model (model=3), in both CPU & GPU version. Instead of using a stick kernel to represent a fibre compartment, a “zeppelin” axially symmetric tensor can be used.
- Updates on ptx2:
- Inclusion of wt_stop masks. Allows streamlines to enter a volume, propagate within, but terminate upon exit. Or for surfaces allow streamlines to cross once, but terminate upon crossing twice.
- Inclusion of —omatrix1 —network option for constructing ROI x ROI connectomes
- Option of outputting Path length as well as Path distribution
- Correction of bugs for surface counting
- FSLeyes - an advanced image viewer with many new features. FSLview has been deprecated, but is still included in this release for legacy purposes.
- ( Beta ) Higher level analyses in FEAT can use randomise instead of FLAME to generate statistics.
( Beta ) MIST - A new and more flexible tool for multimodal subcortical segmentation. The beta release supports segmentation of the putamen, globus pallidus, caudate nucleus and thalamus using T1-, T2- and diffusion-weighted data. For more information, see http://dx.doi.org/10.1016/j.neuroimage.2015.10.013.
( Beta ) MSM - A new tool for cortical surface registration. Registration can use a wide variety of univariate, multivariate and multimodal feature sets. For more information, see http://dx.doi.org/10.1016/j.neuroimage.2014.05.069.
( Beta ) BIANCA - A new tool for automatic segmentation of white matter hyperintensities based on manual training data. The tool is very flexible with respect to input MRI modalities. For more information, see http://dx.doi.org/10.1016/j.neuroimage.2016.07.018.
- ( Beta ) FILM, FLAMEO and MELODIC can run on CIFTI files.
Minor changes have been made to FEAT reporting to make results complaint with NIDM-Results ( http://dx.doi.org/10.1038/sdata.2016.102 )
- The default cluster-forming threshold in FEAT has been changed to 3.1.
- A Fornix template image, kindly provided by Brian Gold, has been added to the atlases.
- A 18-connectivity bug in cluster has been fixed.
- Temporal concatenation in MELODIC now defaults to using MIGP.
- POSSUM has a number of improvements and fixes.
- eddy has been updated
- A bug in FEAT noise-estimation has been fixed
- A subthalamic nucleus atlas has been added, kindly provided by Birte U. Forstmann
- The fslpython environment has been updated, more scripts now use this environment
- Nudge now uses FSLeyes
FSL 6.0 minor release revision history
- eddy has had major features added, along with minor bug-fixes and improvements.
eddy now models how the susceptibility field changes with subject movement. This is described in NeuroImage 171 (2018) 277-295.
- The --slspec parameter can now directly read .JSON output from dcm2niix.
- Two new files are generated, ‘my_output’.eddy_command_txt and ‘my_output’.eddy_values_of_all_input_parameters. These are used by eddyqc, and can be used as a “documentation” of exactly how eddy was run on a given data set.
- fsl_deface, a structural anonymisation script used by the UK Biobank scripts has been added.
- probtrackx2 has been updated ( including probtrackx2_gpu )
- bedpostx_gpu has been restored (after being unavailable in 6.0.0)
- cudimot: a new front-end for implementing GPU-based model-fitting routines has been added.
- BASIL/Oxford_asl (for perfusion quantification using ASL) - new version incorporating new GUI, distortion correction, partial volume correction (for all ASL data), improved registration to structural image, revised inference process, additional kinetic models, ‘white paper’ compliant mode.
- FSLeyes supports loading of complex images, and has more options controlling colour bar display.
- FSLeyes now comes bundled with a copy of dcm2niix
- The latest version of eddy_qc is included.
- An interaction between Armadillo and CUDA causing GPU tools to crash.
- fslcpgeom correctly updates q-form header information.
- fslswapdim now functions as per pre-FSL6.0.0 changes.
- An issue with topup that meant that the estimation of the field was suboptimal
- A rare crash during peristimulus-plot generation has been fixed.
- Images with non-unity scl_slope will be treated as floating-point type.
- Images that incorrectly report the existence of an extension field in post-header bytes ( e.g. created by some Matlab IO routines ) will be read normally rather than reporting an error.
- A standard set of openblas libraries are included in the linux binary downloads. If compiling the sources yourself, you will need to obtain these for your specific system.
- Performance issues with vecreg and mcflirt have been resolved.
- A bug with the -ing option in fslmaths has been fixed.
- When a 4D image is provided to an input intended for 3D images, behaviour has reverted to "FSL5" usage in that the input will be truncated to a 3D volume, with an alert to highlight this has taken place.
- swe: a tool for the analysis of longitudinal and repeated measures neuroimaging data based on the sandwich estimator.
- XTRACT: a command-line tool for automated tractography in humans and macaques.
- Fixed ANALYZE support in fslchfiletype, plus fully report all known formats ( including NIFTI2 ).
- Better fslstats output formatting with atlas masks.
- Allow use of non-continuous atlas mask labels in fslstats.
- Performance improvements.
- Exit gracefully (with relevant error messages) if expected ouput file is not written
- Fixed -B option where skull images were being generated even though not requested
- Fixed nibabel deprecation issue.
- Unified all machine configurations (auto detects most machine differences now).
- Updates for multi-format eddy build.
- FSL build improvements
- Fix compiler warnings.
- Update documentation.
- Update builds for FSL 6.0.x.
- General performance improvements.
- Update fdt GUI to match multi-shell/single-shell defaults.
- Fix model setup wizard for randomise groups.
- Removed interactive coordinate input for img2imgcoord, and img2stdcoord.
- Performance improvements.
- Removed deprecated option in fslreorient2std call.
- Updated help text.
- Added check for matching input image sizes.
- Added check to make sure lesion masks are within white matter mask.
- Added -c (--components) option to save each lesion as a separate image.
- New version of dual_regression.
- New option for choosing optimal slice in slices_summary.
- Only run brainstem training if given correct modalities.
- Fixed build for FSL 6.0.x.
- General performance improvements.
- Added unit tests.
- FSLeyes is now installed via the main fslpython environment.
Eddy configuration script for Linux ($FSLDIR/etc/fslconf/configure_eddy.sh). Automatically sets symlinks to eddy_openmp --> eddy and eddy_cudaX.X -->
- Added fmrib-unpack to fslpython.
- Added pyfeeds to fslpython.
- General improvements.
- Updated boolean option handling for all FSL commandline programs.
- Updates for reordering of parameters.
6.0.3 - [26/11/2019]
FSL 6.0.3 contains minor fixes and updates across a number of FSL programs.
- upgraded to armadillo 9.700
- suppressed cholesky convergence failures
- fslcreatehd: better string handling for descrip field
- fslcreatehd: origin uses FSL coordinate
- limited same size checks to first three dimensions
- switched to using error trap in shell script
- limited same size checks to first three dimensions
- separated LIBS and PROJECTS and sort by required build order
- MATLAB code: fixed intermittent fread bug
- changed b0 unwarping placeholder values to 0.0
- minor bug fixes
- fixed normpdf namespace collision
- fixed namespace collisions
- fixed crash for large number of components
- fixed namespace collision
- fixed issue with byte-swapping ANALYZE files
- added awscli
- updated FSLeyes to 0.31.2
- updated pyfeeds, funpack and fslpy
- fixed bugs related to HR data and several stop/avoid masks in file
- enabled voxelwise design options
- added output of edof if requested
- save dof if requested
- bug fixes and enhancements
- fixed GPU queue bug
- added xtract_viewer
- added ptx_options
- added option to pass probtrackx options as a text file
6.0.4 - [11/08/2020]
- Use enough leading zeros based on number of number of output files, to allow them to be sorted alphabetically (but always at least 4)
- fslcreatehd should always honour FSLOUTPUTTYPE, even if the file already exists
- Add --batim to provide voxelwise ATT estimates
- Updated error trap to new form
- Remove unicode characters
- Fix smoothest verbose printing
- Fixed FWHM reporting
- Switch INC_PROB for legacy projects
- use cfzlib rather than system zlib
- Remove system path from ZLIB defines as causing macports builds to break
- Added fdt/ptx2 rules for master build
- Added variables to control ptx2/fdt during main build
- Switch cuda path for singularity images
- Move libprob.h from the soon-to-be-defunct libprob project into cprob
- Removed legacy/linear images
Rename mist-clean -> mist
rename deface -> fsl_deface
- build zlib for all builds
- The changes to eddy are mainly internal. A lot of effort has gone into speeding up in particular the slice-to-volume motion correction and the movement-by-susceptibility estimation. This effort has focused on the GPU implementation, and you should expect a 2--5-fold speed up depending on what settings you use. As part of the speed-up efforts it has also become more "stable", in that any given update step is much more likely to take us towards the "true solution", and less likely to end up having to be rejected.
- It may seem that those using the non-GPU version of eddy has been short changed in this release. And in a way they have, but in a more important way they have not. The reason that slice-to-volume registration has not been implemented for the CPU/OpenMP version is that we have perceived such an implementation too slow to be practically useful. But a major part of the speed-up of the GPU version has _not_ been more effective code at a detail level, but rather finding new ways of calculating things. And these are equally applicable to the CPU version, so for the next release we envisage CPU-slice-to-vol. Not fast, but bearable.
- update linking order
- Update for FSL 6.0.3 build system
- Fix to trialmode convergence detector so that it still respects max iterations
- Protect calculation of coefficient resels from numerical errors in inference Belt and braces approach
- ignore voxels where we have already had problems and also catch any exceptions. We don't want a run to be stopped just because of a numerical problem here (e.g. non-invertible covariance matrix)
- Try to be more tolerant of bad MVN data when constructing the final result MVN Instabilities during inference may have led to a non-invertible covariance matrix. These voxels are ignored during subsequent inference steps but can cause an exception at the end when we construct the combined params/noise MVN. This protection substitutes zeros when this happens since we have nothing valid for this voxel
- Move log message to avoid confusion - suggests data is being loaded when the file does not exist
- Add option to save variance directly (rather than have to square the STD or get it out of the MVN)
- Fixed data type of evaluate-nt option
- Fixed bug which caused new-style models to write out an empty paramfiles.txt
- Clarify nature of noise parameter being inferred
- Priors consistent with SVB
- Minor addition to priors docs
- Minor tweaks to build instructions
- Clarify that you should try compiling before messing with config
- Too many heading levels...
- Fix broken link
- More detail about setting up FSL dev environment
- change link order
- Hidden option for leadscale value to enable experimentation in future
- Revert previous change to AIF lead in/out scale parameter Gives odd results on test data - to investigate more carefully before making any change
- Relax leadscale to avoid sharp edged arterial bolus
- Remove duplicated member variable what was breaking ARD This variable is defined in the base class and therefore the subclass copy was masking the assignment of ARD to the arterial component
- Add --tiimg option to provide a voxelwise TI image This is handled identically to providing TIs as a list except they are able to vary by voxel. The number of volumes in the image is the number of TIs. Note that PLDs are not supported - it must be TIs
- Change BAT prior to 1.3s which is appropriate with pCASL Multi-TE implies pCASL
- Document sliceband option
- Bugfixes - result sizing gets LFA wrong way round, also incorrect indexing on vector and failure to increment timepoint. (Other than that, fine)
- Add support for variable repeats and multi-band readout
- Add basic documentation
- Removed build scripts which are no longer in use
- Fix incorrect check on number of volumes in data (ignoring repeats)
- Fixed bugs present in previous premature commit!
- Use same defaults as aslrest/oxford_asl for T1, T2, BAT etc.
- Double precision on variables to avoid numerical overflow errors
- Fix typo breaking build
- Clean out of currently unused options and parameters Some of these (e.g. inferring tau, arterial component) may be reintroduced in the future but the existing code is not functional and is easily re-written as necessary - no need for it to clutter up the model at present
- Support variable tau values
- Tweaks to improve fitting to test data. Initialize phase from minimum rather than maximum as it is generally more specific. Also relax prior on phase and clarify restriction of range of phase in evaluation. Now fits test data nicely
- Ignore test output (and remove file added in wrong place!)
- Ignore test output
- Updated multiphase test and put in own dir
- Document all used options
- Fix multiple errors in log when using --save-model-extras This is because the AIF output does not typically have the same number of output volumes as the data.
- Add multi-TE model, refactored to new API from Federico's code
- change link order for FSL 6.0.4
- Remove commented out old code
- Remove old build script no longer in use
- Add placeholder documentation
- Correct option type for fa and tr, plus improve log output a bit
- Minor stylistic changes to new steady shape code
- Document lineshape option
- change link order for FSL 6.0.4
- New priors based on literature value
- Remove old misleading comment
- Correct option name for AIF T1 value
- change link order for FSL 6.0.4
- Roll back on previous changes - do not try to clamp parameters to sensible limits This is largely pointless since by clamping the parameter values we ensure that the gradients are zero - so if the parameter gets into this range it will never get out. Instead we have added more robust protection against numerical errors to the fabber core.
Restrict CBF and ABV to >= 0 to avoid numerical problems in nonbrain voxels Would prefer to let the model recover from this itself but it seems to struggle to do so.
- Clarify that delt is actually in seconds not minutes Tweak priors to avoid instability caused by very very uninformative priors Numerical warnings should be displayed only once per evaluation
- Add initialization method for voxel posterior
- Initialize sig0 parameter from first data point Also tweak prior mean for cbf so we can add a log prior without redefining the mean
- Remove references to Verbena in theory section
- Add image
- Initial documentation
- change link order for FSL 6.0.4
- Remove old build scripts not needed any more
- Add basic documentation - mostly placeholder for now.
- Re-order parameter extraction to allow for change in parameter order
- Make sure all opts have a documentation string Put sig0 as first parameter as its the main one that willl always be included
- change linking order
- add -db flag to set maximum offset in b-value
- select_dwi_vols fix requested by MC
- Update dtifitOptions to describe --kurtdir output
- remove mean kurtosis map (--kurt produces a nicer map)
- Raise errors of incompatible flags before reading the data
- Raise error if --wls and --kurtdir flags set
- back to 1% of S0 as minimum signal
- add prior to kurtosis values
- allow lower minimum signal when fitting full kurtosis model
- optionally use weighted least square for --kurtdir
- fit 3 kurtosis components
- set minimum signal to 0.01
- S0 like in original fit
- recompute eigen-values, FA, and mode
- fix angular dependence of kurtosis
- actually use the --kurtdir flag
- document new Amat function
- Use standard master rule eval
- Remove fslconfig dependency
- Fix when to report non-parametric
- Fix assignment to handle odd number of time points - use miscmaths pinv
- Use MNI152-named version of mask
- change python env to fslpython - changes for more interp choices, updated options/usage and modified 3D option arg.
- FSL-MRS: an end-to-end tool for MRS data analysis, including data conversion, basis simulations, FID processing, fitting, quantitation, and visualisation
- Added option to write out full Jacobian matrix
- RF: Changes to allow libgdc to be compiled as a self-contained shared library.
- don't force varnorm flag if --keep_meanvol set
- Remove MELODIC from stage 4 thresholding code
- Simplify z-stat thresholding
- Stop removing intermediate zstat maps
Remove sleep statement
- change python env to fslpython
- removed use of Profiler to break dependency on utils
- Compile all with CXX11
- Made changes to Levenberg-Marquardt (levmar) so that there is now a pure Gauss-Newton option
- Change make to use C++11 and added profiler to levmar in nonlin
- If the SVD in the default pinv call fails, re-call with std method
Revert INC_PROB-> INC_CPROB, because miscvis depends on miscmaths, which has not been updated
- add fsl/sliceanimate use CPROB rather than PROB
- Migrate fslanimate/sliceanimate from avwutils into miscvis, to remove circular dependency between the two projects.
- fix read error where an extension is in path
- Allow newimage cog to use all intensities or val-min intensitites
- change byteswap from 8 to 2
- Avoid using zlib autodetect on img data blocks due to risk of false positives
- Replace subprocess.check_output with python2.6 friendly version for centos 6
- Allow for possibility of modifying minimum base PVE for WM/GM
- Support the new --tiimg option to pass TIs as a voxelwise map
- CHange in location of linear MNI template for FSL 6.0.4+
- Fix for FSL build
- Protect against NaN values in i2 calculation and output floats to 2 d.p.
- Allow GM and WM 'pure' thresholds to be user-specified Voxels with at least this much GM/WM are included in ROIs designed to capture GM/WM perfusion
- Split output into separate files for overall perfusion, GM and WM plus add gm and wm threshold options
- Add generation of regionwise statistics
- Constrain the Jacobian to try to avoid negative values Negatives don't make much sense geometrically and result in negative perfusion values when using voxelwise calibration
- Add support for --batim - voxelwise ATT estimates to be passed to Basil
- Boost font size - it is particularly small on Mac
- Tweak label to try to make sure update button is visible on Mac
- Improve proportion of space assigned to preview windows
- Fix disabling of IAF (tag/control) choice - no longer needed
- Move WP compatibility widget to analysis tab and make accessible by checkbox
- Allow extra widgets after a checkbox
- UI tweaks - label for grouping option and give straightfowrward choice for TC pairing options
- Use recommended method to exit app on close clicked
- Fix missing import cause error on Mac
- Keep 'running please wait' message until run completes
- Re-order links in white paper widget and make sure they are enabled/disabled correctly
- Display TI/PLD as required when casl/pasl selected
- Fix - make asl_file do subtraction where required
- Update options after GUI completely set up
- Add Layout() call to make sure number lists are displayed correctly at startup
- Update GUI after calib enabled as it may be done by the WP widget
- Remove debug message
- Add exchange and dispersion options
- Rationalize layout to work better with white paper widget and run button
- Fix white paper mode to control T1 and BAT
- Fix for change to main() function in gui
- Include all bitmaps
- Clarify use of matplotlib
- Add other bitmaps used in gui
- Switch fsleyes for matplotlib
- Add Conda build recipe - potentially better route for FSL install
- Add FSLeyes as preview widget plus various bugfixes and add icon
- Merge branch 'master' into newgui
- Remove autogenerated file
- First attempt at new gui
- Fix python install - now versioned in setup.py
Issue #8: Fix typo: asl2struct rather than asl2struc THis would affect output of the asl->std transformation in the case where the struc->std transform was supplied as a matrix (normally it's a nonlinear warp which is not affected by this)
- Add support for variable repeats and reformat as a standard Python module In the future we may want to pip install this or make a conda recipe
- Issue #8: Handle case where FSLOUTPUTTYPE is set to NIFTI rather than NIFTI_GZ THis is only really a workaround - the longer term solution is to move to fslpy which handles all this transparently
- Use informative noise prior if there are 5 of fewer timepoints Previously this was enabled by default only if you had a single timepoint but it causes an issue for data with small numbers of timepoints generally so relax this a bit.
- Need to pass repeats string to asl_file when re-ordering ASL data after distortion correction
- Fix bug preventing re-generation of mask during PVC
- Output and calibrate WM variance in partial volume runs
- update miniconda URL
- Added FSL_MRS 1.0.3
- Added TIRL 2.1.2b1
- FSleyes+fslpy to latest
- Copy, don't sym-link, .app bundles, to avoid macOS .app caching errors. Drop fslview.app/assistant.app - now only FSLeyes.app is placed into /Applications/.
- eddy_qc to 1.0.3
- Add channels to fslpython env, use verbose flag when creating environment
- explicitly list pip
Change channel priority to conda-forge > defaults > FSL. Use strict channel priority to enforce this.
- Bump up retry backoff factor - can't hurt
- update configure_eddy.sh to also check for installed cuda in /usr/local/cuda
- Tell curl to follow redirects
- Make fslpython install errors more prominent
- Added Nearest neighbour interpolation
- Use standard master rule eval
- Remove fslconfig dependency
- Use MNI152-named version of template
- Make consistent indenting (remove all tabs)
- Fix usage for -m option, which incorrectly references *stdmask
- "Tensor Image Registration Library v2.1 (beta): a Python-based general-purpose image registration framework with prebaked scripts for registering stand-alone histological sections to volumetric MRI data."
- CXX11 Changes for Centos6
- Added some includes needed for build on CentOS
- Added initialisation of class static variables
- Added FSLProfiler class
- Add log CBF option
- Add --allow-bad-voxels. The DSC model is prone to numerical instability and this can help allow a run to complete even with some non-fitting voxels (e.g. when the mask includes nonbrain voxels)
- Removed theory page - now hosted in FABBER_DSC docs
- Reference theory section from FABBER_DSC documentation
- Added functionality to allow fnirtfileutils to write full jacobian matrix
- Update Makefile
- changes to readme
- Updated xtract_data location to FSLDIR/data
- Added xtract_stats
- Added reference space tractography functionality
- Added '-list' flag to show tract names. Added option to select a subset of the pre-defined tracts from either Human or Macaque - user provides structure file with tract names or tract names and nsamples. Small bug fixes
- Changed order of fsl_sub -T and -q args to overcome fsl_sub queue selection issue
- Updated to reflect xtract_viewer changes
- Added species flag
- Added CPU time allocation of 1.5 days
- Update README
- Small changes to ILF and FX protocols to remove false positives
- Removed PTR from Macaque protocols
- add new CFLAGS
- use --static for all builds now
- add latest non-gpl cloudflare zlib