Differences between revisions 96 and 97

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 )
The version of eddy is the same as in 5.0.11. A new version of eddy will be released with FSL 6.0.1
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.
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 5.0 minor release revision history

5.0.1, 01/10/2012

Fixed critical scripting issues with FEAT
Fixed post-hoc output timecourses in MELODIC
Minor fixes to a small number of source files

5.0.2, 11/12/2012

Numerous minor bug fixes
Added Subthalamic Nucleus Atlas, courtesy of Birte Forstmann

5.0.2.1, 03/01/2013

fsl_sub patch

5.0.2.2, 15/02/2013

FSLview patch for HCP
Harvard-Oxford subcortical atlas fix

5.0.3, 07/05/2013

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

5.0.4, 10/05/2013

Fixed an issue with MELODIC Group ICA introduced in 5.0.3
Changes for HCP pipeline compliance
Updates to some atlas definitions

5.0.5, 15/10/2013

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.

5.0.6, 09/12/2013

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.

5.0.7, 14/07/2014

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

5.0.8, 04/12/2014

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.

5.0.9, 29/09/2015

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.
BASIL:
- 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

5.0.10, 25/04/2017

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.

5.0.11, 23/03/2018

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

6.0.1, 11/03/2019

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.

6.0.2, 29/09/2019

General

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.

New tools

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.

avwutils

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.

basil

Performance improvements.

bet

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

bianca

Fixed nibabel deprecation issue.

config

Unified all machine configurations (auto detects most machine differences now).
Updates for multi-format eddy build.

distbase

FSL build improvements

fabber

Fix compiler warnings.
Update documentation.
Update builds for FSL 6.0.x.
General performance improvements.

fdt

Update fdt GUI to match multi-shell/single-shell defaults.

feat

Fix model setup wizard for randomise groups.

flirt

Removed interactive coordinate input for img2imgcoord, and img2stdcoord.

fsl_deface

Performance improvements.
Removed deprecated option in fslreorient2std call.

lesion_filling

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.

melodic

New version of dual_regression.

miscvis

New option for choosing optimal slice in slices_summary.

mist

Only run brainstem training if given correct modalities.

MSM

Fixed build for FSL 6.0.x.

oxford_asl

General performance improvements.
Added unit tests.

post_install

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 -->

eddy_cuda

Added fmrib-unpack to fslpython.
Added pyfeeds to fslpython.

sgeutils

General improvements.

utils

Updated boolean option handling for all FSL commandline programs.

verbena

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.

armadillo

upgraded to armadillo 9.700
suppressed cholesky convergence failures

avwutils

fslcreatehd: better string handling for descrip field
fslcreatehd: origin uses FSL coordinate

basisfield

limited same size checks to first three dimensions

bet2

switched to using error trap in shell script

cudabasisfield

limited same size checks to first three dimensions

distbase

separated LIBS and PROJECTS and sort by required build order

etc

MATLAB code: fixed intermittent fread bug

feat5

changed b0 unwarping placeholder values to 0.0

fsl_deface

minor bug fixes

libvis

fixed normpdf namespace collision

melodic

fixed namespace collisions
fixed crash for large number of components

mm

fixed namespace collision

NewNifti

fixed issue with byte-swapping ANALYZE files

post_install

added awscli
updated FSLeyes to 0.31.2
updated pyfeeds, funpack and fslpy

ptx2

fixed bugs related to HR data and several stop/avoid masks in file

swe

enabled voxelwise design options
added output of edof if requested
save dof if requested
bug fixes and enhancements

xtract

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]

avwutils

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

basil

Add --batim to provide voxelwise ATT estimates

bet2

Updated error trap to new form

bianca

Remove unicode characters

cluster

Fix smoothest verbose printing
Fixed FWHM reporting

config

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

cprob

Move libprob.h from the soon-to-be-defunct libprob project into cprob

data_standard

Removed legacy/linear images

distbase

Rename mist-clean -> mist
rename deface -> fsl_deface
build zlib for all builds

eddy

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.

fabber_core

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

fabber_models_asl

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

fabber_models_cest

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

fabber_models_dce

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

fabber_models_dsc

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
Updates
Add image
Initial documentation

fabber_models_qbold

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

fdt

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

feat5

Fix when to report non-parametric

film

Fix assignment to handle odd number of time points - use miscmaths pinv

first

Use MNI152-named version of mask

flirt

change python env to fslpython - changes for more interp choices, updated options/usage and modified 3D option arg.

FSL_MRS

FSL-MRS: an end-to-end tool for MRS data analysis, including data conversion, basis simulations, FID processing, fitting, quantitation, and visualisation

fugue

Added option to write out full Jacobian matrix

libgdc

RF: Changes to allow libgdc to be compiled as a self-contained shared library.

melodic

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

misc_scripts

change python env to fslpython

miscmaths

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

miscvis

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.

newimage

fix read error where an extension is in path
Allow newimage cog to use all intensities or val-min intensitites

NewNifti

change byteswap from 8 to 2
Avoid using zlib autodetect on img data blocks due to risk of false positives

oxford_asl

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
Updated
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
Updated
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

post_install

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

ptx2

Added Nearest neighbour interpolation
Use standard master rule eval
Remove fslconfig dependency

siena

Use MNI152-named version of template
Make consistent indenting (remove all tabs)
Fix usage for -m option, which incorrectly references *stdmask

TIRL

"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."

topup

Fixed checking bounds for MoveMatrix and MovePar
Fixed check for indexing past last volume

utils

CXX11 Changes for Centos6
Added some includes needed for build on CentOS
Added initialisation of class static variables
Added FSLProfiler class

verbena

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

warpfns

Added functionality to allow fnirtfileutils to write full jacobian matrix

xtract

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

xtract_data

$FSLDIR/data/xtract_data
Update README
Small changes to ILF and FX protocols to remove false positives
Removed PTR from Macaque protocols

zlib

add new CFLAGS
use --static for all builds now
add latest non-gpl cloudflare zlib

6.0.5 - [20/07/2021]

asl_mfree

Added README and LICENSE for completeness

avwutils

RF: Migrate the distancemap tool from tbss to avwutils
DOC: Update usage
BF: fslcreatehd was not populating intent fields
RF: More precise num-args check
RF: Remove use of no-longer-existing fslcreatehd -r option
RF: fslcreatehd: set number of dimensions sensibly
STY: Fix indentation

basil

Ensure that the T1 parameter is included in the model if --t1im is specified, even if --infert1 is not --infert1 will allow the T1 image to vary, otherwise it is treated as ground truth. This is handled by manipulating the precision on the prior within the model
Remove old debug message

bet2

RF: Make d parameters hidden for now
MNT: Comment regarding d1/d2 type
MNT: int64_t -> double to match current bet2 results
ENH: Improved 2D "mode"

bianca

MNT: make sure bianca_perivent_deep gets installed to $FSLDIR/bin
Handle UTF-8 files with BOM
Added script bianca_perivent_deep for subclassification of pvent and deep lesions
replaced deprecated get_data with get_fdata()

config

Added 10.2 to eddy CUDA build
RF: Allow supportedGencodes.sh script to be overridden by FSLCONFDIR
MNT: Remove 11.2 target for Centos 7 compat
Added JIT build also to default branch
MNT: Added CUDA SDK 11.2 to list of builds for eddy
Added CUDA versions 11.0-11.2. Also added a JIT build to ensure forwards compatibility of any executables.
Added support for CUDA 10.1

data_atlases

ENH: Update from 28/12/2012 release

data_atlases_xtract

SW macaque atlas update

distbase

MNT: Build the fabber pet module

eddy

Removed openmp parallellisation from write_jac_registered_images
Fixed bug that made CPU-slice-to-vol crash when no topup was provided
Uncommented openmp pragma in write_jac_registered_images
Changed the way the EC and susc fields are combined for the scan2model transforms.
More debugging and refactoring related to slice-to-vol for CPU
Ongoing debugging of slice2vol for CPU. Changed how interpolation parameters were passed to GPU branch of slice2vol
Ongoing debugging of slice2vol for CPU
Added EddyTry/EddyCatch to a number of functions where they were missing
Removed check that disallowed slice-to-vol for the CPU version
All options for slice-to-volume resampling implemented. First version that compiles
CPU version now able to calculate mixed derivatives for slice-to-volume
Fixed a problem with debug output in the CPU build
ENH: Laxer check for sameness of voxel sizes. As as new criteria in newimage.
Added routines to write out outliers only. Potentially useful for debugging.
Made sure that predictions are correctly scaled when written
Made sure that cublas_v2.h was included before anything else
Added files with low level CUDA utility functions
Changes that allows me to write out predictions in scan space
Better error reporting for CUDA/cuBLAS errors.
Changes to GetSuscHzOffResField for when estimating move-by-susc without a static field
Added more checks in InitGpu to provide more informative error messages
Added option to specify compute capability to Makefile

etc

MNT: Update version to 6.0.5

fabber_core

Rationalize spatial prior calculation to avoid multiplying and later dividing by 8
Add newlines at end of files to remove compiler warning
Only log mean value on first load Otherwise we get this reported for every voxel when using an image prior since the image prior now informs the initial posterior
Add undocumented expert-option to tweak prior on spatial precisions
Switch to Apache2 license
Issue #6: Make initial posterior value equal to voxelwise value when we have an image prior
Minor clarity to comment
Correct references to old web site
Fix includes for new FSL build system
Fix warning about multi-timepoint data. The main data is generally 4D so we should open it as 4D even when we just want the 3D extent

fabber_models_asl

added copy right text
Modified CBF equation
updated default T2 blood values
Corrected some error. Added TE correction
added some comments
VS ASL
Switch to Apache2 license
Update README.md
Minor logfile fix
Fix includes for new FSL build system
Add option for WM partition coefficient rather than purely hardcoded

fabber_models_cest

Add options for custom water T1/T2 for CESTR* calculation only This is independent of the priors in the poolmat which will be used for CESTR* as well if these options are not given
Switch to Apache2 license
Fix includes for new FSL build system

fabber_models_dce

Switch to Apache2 license
Fix includes for new FSL build system
Rationalization of priors so they are consistent and sensible in all models
Updated docs

fabber_models_dsc

Switch to Apache2 license
Fix includes for new FSL build system

fabber_models_dualecho

Switch to Apache2 license
Fix includes for new FSL build system

fabber_models_dwi

Switch to Apache2 license
Fix includes for new FSL build system

fabber_models_qbold

Switch to Apache2 license
Updated to work with new FSL build system

fabber_models_t1

Switch to Apache2 license
Fix includes for new FSL build system

fdt

BF: move wildcard out of quotes
STY: Remove all tabs, fix indentation
BF: Fix improperly quoted command
RF: Concatenate arrays with += syntax
BF: Correctly concatenate array options
Fix compilation issue with limits.h
Switch to bash arrays for arguments
Convert to using arrays for command building Quote as many variables likely to hold paths as possible Don't execute output of fsl_sub --has_coprocessor='cuda'!
Modern command capture Call GPU version earlier to ensure arguments not dequoted
Quote variables
White space clean up
Check for GPU hardware or queues - error if none found
Add time to single_slice jobs Make job times configurable by variables
Ensure fsl_sub called as FSLDIR/bin/fsl_sub
Error messages should go to stderr
Use -n not ! -z
Make sure fsl_sub is called as FSLDIR/bin/fsl_sub
Ask fsl_sub if it has a cluster
Ask fsl_sub whether it has a cluster Ask fsl_sub whether it has CUDA Get fsl_sub to delete jobs
More rm quoting
Don't mail the user
Remove hard coded queue name
Make rm safer
Switch to new fsl_sub

feat5

BF: Fix for overflow bug

flirt

Switch to simpler imcp use
set tdim on outpout vol to match flirt.cc applyxfm

fslsurface

Merge branch 'mnt/libprob' into 'master'
MNT: Include cprob/libprob.h instead of including libprob.h directly
Merge branch 'mnt/remove-opengl' into 'master'
MNT: Remove friend refs to fslsurfacegl
MNT: Remove obsolete junk from makefile
MNT: Remove unused/obsolete structs which use GL types, and references to GL
STY: Consistent indentation
Merge branch 'bf/readGIFTI' into 'master'
BF: Explicit instantiation of readGIFTI is required, otherwise implicit instantiations may be inlined during optimisation
STY: whitespace

fugue

BF: Make sure convertwarp correctly sets the sform/qform of the output displacement field according to the provided reference image
STY: whitespace

lesions

Revert "add lesion split program. it splits a binary lesion mask into multiple lesions if multiple disconnected commonents exist"
add lesion split program. it splits a binary lesion mask into multiple lesions if multiple disconnected commonents exist
make white matter mask optional

melodic

RF: in>0 not valid for modern compilers

meshclass

MNT: Removed irregular symbol from comment
ENH: Added anisotropic rescale

misc_c

TEST: Resolve sym-links
MNT: Remove C version of tmpnam
TEST: pyfeeds unit tests for tmpnam
RF: Port tmpnam to python
DOC: Logic for tmpnam
BF: Fix and streamline tmpnam/TMPDIR changes
RF: Hopefully simplify logic
use TMPDIR if set

misc_tcl

Remove SGE hard dependency Update usage comment to reflect that this isn't SGE only now

miscmaths

MNT: Include cprob/libprob.h instead of including libprob.h directly

mist

Removed hardcoded queue names

newimage

MNT: invalidateSplines is more grammatical
MNT: rename negateSpline
MNT: Missing semicolons
BF: Invalidate splines on non-const dereferences
ENH: Revised samedim logic
BF: Explicit instantiations of readGeneralVolume are required, as implicit instantiations may be removed/inlined by optimisation
ENH: Extensions are now a basic property ( for copying )

NewNifti

RF: Whitespace
RF: Simplified after re-read of standard wording
MNT: Renamed member
MNT: datumByteWidth needs to be const
RF: Renamed method
ENH: more robust determination of data-width

oxford_asl

Move generation of WM tissue segmentation to before first registration in case we are doing BBR for reg 1
Remove test for registration before trying to copy registration QC files This will mean warnings in the log if these files don't exist but it seems in UKB that the test is not working correctly
Move calculation of bias field/sensitivity map in ASL space until after registration This fixes a bug caused by reordering of registration steps because we can't put the sensitivity map in ASL space until we have the struc2asl registration. Also minor log re-ordering for cosmetic reasons
Add option to save region analysis ROIs/masks
Naming - refer to 'cerbral WM' not 'cortial WM'
Allow multiple custom MNI atlases
Add option to save structural space ROIs and handle case where don't have both GM and WM PVE maps
Add cortical GM/WM ROIs to region analysis script
Change MNI atlas option to add regions to standard atlas rather than replacing them
Add automatic masking of subcortical regions in GM/WM ROIs and generate separate stats for these ROIs
Fix typo in capturing output of initial registration
Make sure QC output is BBR registration in case where we use BBR in initial
Add option to use BBR on initial registration This also involves reordering the segmentation to be before the registration
Ignore voxels where variance is zero This occurs typically as a failure of extrapolation of the calibration image in voxelwise calibration. Normally the perfusion is also zero which means the averages will be biased and the precision-weighted mean will be zero or close to it.
Increase degree of dilation to cope with poor initial registration
Protect against non-existant GDC warp file THis is a bit random but is useful in UKB as the script which generates the warp does not always seem to work! And in the end a sanity check does no harm here
Clarify log message to indicate the source of the structural data if not FSL_ANAT
QC output - include motion parameters and simple plots plus calibration image in structural space Also fix accidental botching of some of the other registration QC output in previous commit.
Merge stdout and logfile stream into a single log which is sent to both. Previously some messages went to stdout and some to the logfile. I will obviously miss the fun of trying to figure out how these message interleave in real time, and of having to ask users to provide both the stdout and the logfile, but probably not that much.
Provide option for explicit specification of the registration reference image
Warn if Basil mask did not include all the voxels in the final analysis mask
Support the use of a dilated mask for BASIL analysis. Final output now all uses the same mask which is that derived from the final registration. Previously PVC outputs used this mask but non-PVC outputs used the original mask
When generating ROI stats from a PVC run, use the same mask for the stats as used for the analysis On a PVC run, the mask is regenerated from the improved final registration and that is what's used for the PVC Basil run. So when we are generating statistics from these outputs we should use the same mask as used in basil
Add option to use a label image as an ROI atlas The region analysis script has the ability to use multiple atlases but for simplicity we restrict oxford_asl to the ability to use either the FSL standard atlas or a single label image atlas
Fix problem identified in UKB where incorrect Python is used when FSLDEVDIR is not set This occurs because on some systems /bin/python exists. To avoid using this, check to see if FSLDEVDIR exists before using it.
Fix comparison to work with POSIX-standard bc Previous code relied on GNU extensions to allow evaluation of a boolean expression directly
Added --qc-output and initial set of additional outputs for quality control
Switch to Apache2 license
Prevent pipeline failing when fieldmap warp contains NaN values THis can happen occasionally but typically only outside the ASL image area
When fslpython does not exist (e.g. in UKB) attempt to fall back on regular python This will only work if the user has the required libraries installed, i.e. fslpy, so we generate a warning in this case
Make sure ROIs are masked with the brain mask so we don't accidentally include any voxels which have not been fitted by basil
Support region analysis without --fslanat provided we have struc->std warp and struc image
Handle version failure better for cases where we are not in a git repo
Document --fa option
Merge branch 'master' of https://github.com/ibme-qubic/oxford_asl
Add artonly option as per basil
Merge pull request #11 from hanayik/master
update call for latest FSLeyes embed

post_install

MNT: FSLeyes to latest
BF: fsl_sub script handling
CI: work if TMPDIR is unset
MNT: Minor updates to fsleyes, fslpy. New version of fsl_add_modue. Initial release of fsl_get_standard.
MNT: Stick with wxpy 4.0.7
CI: Use shell runner - job was being dispatched to macOS docker runner, and hence running in linux
CI: File tests use single bracket operator in bash
MNT: Update expected #lines for progress update
MNT: Passing the -v/--verbose flag actually suppressees the download progress output, so it's better to call without -v for the sake of a more useful progress update.
CI: Run test script with bash
CI: Wasn't finding log file on macos
MNT: Add nilearn (#5)
MNT: Bump FSLeyes to latest
Added fsl_sub sge for internal branch only
Added fsl_sub
MNT: Update various packages to resolve dependecy issues
MNT: Update scipy for fsl_mrs
ENH: Latest fsl_mrs from WC
make eddy setup less chatty
change application install location if not root
TEST: bug
TEST: typo
RF,BF: Added paramiko+pyyaml back in, fixed TIRL package name, use nidmresults conda packages instead of installing via pip
TEST: Test fslpython_install on macOS, adjust to run in either shell or docker runnesr
RF: Remove implicit "non-sciency" dependencies. Bump Python to 3.8. Bump all core dependencies to latest available.
BF: fix path
BF: fix path
CI: need libgl to install fslpython env
CI: dump install log
CI: install basic utils
CI: Test fslpython installation on new commits
MNT: bump funpack to latest, add fsl-add_module
MNT: fslpy and funpack to latest
MNT: fsl_mrs to 1.0.5
MNT: Remove tabs
RF: Only support linking to files
DOC: typo
DOC: fixed some typos in comments
R: Change link/unlink scripts so they create wrapper scripts instead of symlinks

ptx2

RF: More explicit down-casts, to avoid errors on strict compilers
RF: Explicitly down-cast from double to float, to avoid errors on strict compilers
STY: Consistent indentation
MNT: include cprob/libprob.h rather than libprob.h
RF: Disambiguate round

qboot

BF: reference persistence not guaranteed
MNT: include cprob/libprob.h rather than libprob.h
Update for new fsl_sub

randomise

BF: Existing quoting prevented wildcard expansion
Update for new fsl_sub
OPT: Quote for safety
More BASHification
Modernise and convert to BASH
BF: Removed debug text from --skipTo setup

tbss

Merge branch 'rf/move-distancemap' into 'master'
RF: Remove distancemap * it is being moved to avwutils

verbena

Handle case where FSLDEVDIR is not set - do not add /bin the the path ahead of everything else!
Expose options to save model fit and residue function

warpfns

Cleaned up debug code
Only reinitialise in apply_warp if size of input mask is wrong
Debug version
Printouts so I can see if the right sources are used
Changes logic in raw_general_transform to avoid &= construct

xtract

Merge branch 'xtract_blueprint' into 'master'
Xtract blueprint
Merge branch 'wayorder' into 'master'
Added wayorder option to allow for specific target ordering
Merge branch 'bug-allow-noninteger' into 'master'
Bug allow noninteger
Merge branch 'master' into 'master'
Quote strings with variables within
Add support for new fsl_sub
Merge branch 'CUSTOMspec' into 'master'
Added -species CUSTOM option to allow tractography in any species

6.0.5.1 - [08/11/2021]

oxford_asl

Hot-fix for bug in FSL 6.0.5 - can cause second registration to fail

6.0.6 - [22/11/2022]

CHANGELOG 6.0.6.md

6.0.6.1 - [05/12/2022]

CHANGELOG 6.0.6.1.md

6.0.6.2 - [04/01/2023]

CHANGELOG 6.0.6.2.md

6.0.6.3 - [01/03/2023]

CHANGELOG 6.0.6.3.md

6.0.6.4 - [09/03/2023]

CHANGELOG 6.0.6.4.md

6.0.6.5 - [12/05/2023]

CHANGELOG 6.0.6.5.md

6.0.7 - [14/07/2023]

New Tools

mmorf - The MultiMOdal Registration Framework. For simultaneous, nonlinear alignment of multimodal image data.
fsl-nets - New Python-based re-implementation of the MATLAB FSLNets scripts, for FMRI network modelling
file-tree - Framework to represent structured directories in Python
fsl-pipe - Declarative pipelines based on file-tree
bet4animal - species-tuned BET, kindly provided by Takuya Hayashi

CHANGELOG 6.0.7.md

6.0.7.1 - [18/07/2023]

New Tools

fsl_prepare_fieldmap - Now supports GEHC fieldmaps, kindly provided by Brice Fernandez

CHANGELOG 6.0.7.1.md

6.0.7.2 - [22/08/2023]

Highlights

**New** FSLeyes MRS plugin - for working with MRS data from within FSLeyes
**New** spec2nii command-line tool - for generating MRS NIfTI images
fsl_mrs 2.1.12 - A range of bug fixes and improvements
Fixed threading initialisation issue in some FSL tools
FSLeyes 1.8.0 - New lightox options to overlap slices, and reverse slice order. A range of other bug fixes and improvements.
fsl-nets - fixed bug in the plot_spectra function.
newimage - Suppress some debug messages, fixes to .hdr/.img file extension handling
fslstats - new -json option for JSON-formatted output

CHANGELOG

6.0.7.2.md

6.0.7.3 - [05/09/2023]

Highlights

Fixed some issues with the fslchfiletype command
immv/imcp honour $FSLOUTPUTTYPE more closely
FSLeyes - minor bug fixes and new --cmapCycle command-line optionimprovements.

CHANGELOG

6.0.7.3.md

6.0.7.4 - [29/09/2023]

Highlights

FSLeyes 1.9.0 - Updates for compatbility with newer versions of matplotlib; new "FSLView" mode for viewing legacy data sets.
FSL-MRS 2.1.13 - Add group level f-tests to the fmrs_stats tool.
New open_fsl_report command for opening PNM HTML report files.

-  ⇤ ← Revision 96 as of 16:11:03 08-02-2024 → 
  Size: 73461
  Editor: MatthewWebster
  Comment:
+   ← Revision 97 as of 16:11:20 08-02-2024 → ⇥
  Size: 73464
  Editor: MatthewWebster
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1297:
-No change to FSL packages
+ * No change to FSL packages