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