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
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