BUG
- sct_qc: Fixed corruption of QC json file when running parallel jobs. View pull request
- sct_label_vertebrae: Fixed bug that appeared when inputing uncompressed nifti file. View pull request
- sct_label_vertebrae: Fixed bug in the post processing of detect_c2c3. View pull request
- sct_propseg: Fixed ignored -init flag and minor improvements. View pull request
- sct_deepseg_lesion,sct_deepseg_sc: Fixed bug and clarified usage of -centerline viewer. View pull request
- sct_dmri_moco,sct_fmri_moco: Work around "too many open files" by slurping the data. View pull request
- sct_straighten_spinalcord: Fixed crash caused by wrong estimation of centerline length in case of incomplete segmentation. View pull request
- sct_extract_metric: Fixed bug in method max. View pull request
- sct_flatten_sagittal: Fix bugs related to image scaling. View pull request
- sct_label_vertebrae: Fixed path issue when using -initlabel flag. View pull request
- sct_get_centerline: Convert data to float before intensity rescaling (in optic). View pull request
- sct_deepseg_lesion,sct_deepseg_sc: Fixed ValueError and IndexError. View pull request
- sct_register_to_template: Fixed regression bugs. View pull request
ENHANCEMENT
- Clarify handling of logger, error and exceptions. View pull request
- msct_register,sct_register_multimodal,sct_register_to_template: Refactoring to allow use of im AND seg in the registration process. View pull request
- sct_get_centerline,sct_straighten_spinalcord: Increased smoothness of default bspline centerline fitting algorithm . View pull request
- sct_get_centerline: Remove Optic temp files by default. View pull request
- sct_qc: Lock qc report during generation. View pull request
- sct_process_segmentation: Major modifications to simplify usage and fix various issues with shape analysis. View pull request
- sct_process_segmentation: Minor fix in usage and csv output. View pull request
- sct_warp_template: Faster execution and other minor improvements. View pull request
- sct_qc: Various improvements on the QC report and resampling module. View pull request
- sct_process_segmentation: Major refactoring of centerline routine. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_label_vertebrae: Removed support for -initc2 flag because there is an alternative approach with sct_label_utils. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_extract_metric: Expose aggregate_slicewise() API and various improvements. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_register_to_template: Updated PAM50 template header to be in the same coordinate system as the MNI template. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_qc: Various improvements. View pull request
- sct_deepseg_lesion,sct_deepseg_sc: deepseg_sc: Speed processing up . View pull request
- sct_qc: QC now scales images based on physical dimensions (previously based on voxels). View pull request
- sct_process_segmentation: Major refactoring to bring few improvements. WARNING: Breaks compatibility with previous versions of SCT. View pull request
FEATURE
- sct_qc: New API to generate QC reports. View pull request
- sct_label_vertebrae: Added possibility to rescale intervertebral disc distance and various improvements. View pull request
- sct_register_to_template: Now possible to specify the type of algorithm used for cord straightening. View pull request
- sct_label_vertebrae: spinalcordtoolbox/vertebrae/detect_c2c3 -- New module. View pull request
- sct_compute_snr: Now possible to output SNR map, removed requirement for inputing mask, and few other improvements. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_dmri_separate_b0_and_dwi: sct_dmri_separate_b0_and_dwi: Now append suffix to input file name to prevent conflicts. WARNING: Breaks compatibility with previous versions of SCT. View pull request
- sct_smooth_spinalcord: Enable to set smoothing parameters in all axes. WARNING: Breaks compatibility with previous versions of SCT. View pull request
DOCUMENTATION
- sct_label_vertebrae: Updated documention on how to create vertebral and disc labels. View pull request
- sct_changelog: Few improvements on automatic Changelog generation. View pull request
INSTALLATION
- Using Python 3.7 for default installation. View pull request
- Fixed installation error caused by old SSL module. View pull request
- First pass at also supporting pip installations. View pull request
TESTING
- sct_deepseg_lesion,sct_deepseg_sc: deepseg_sc and _lesion: add new unit tests. View pull request
BUG
- sct_fmri_moco: Fixed regression bug related to the use of a mask View pull request
- msct_nurbs: Fixed singular matrix error View pull request
ENHANCEMENT
- sct_extract_metric: Do not zero negative values View pull request
BUG
- sct_propseg: Reordered variable assignment View pull request
- sct_straighten_spinalcord: Fixed AttributeError related to conversion of numpy array to list View pull request
- sct_create_mask: Few fixes and improvements View pull request
ENHANCEMENT
- sct_get_centerline: Use the new viewer View pull request
- sct_fmri_moco: Generalize motion correction for sagittal acquisitions and other improvements View pull request
FEATURE
- sct_straighten_spinalcord: Few fixes and improvements View pull request
- sct_deepseg_sc/lesion: Allow to input manual or semi-manual centerline View pull request
BUG
- Updated URL for PAM50 View pull request
- sct_register_to_template: Fixed wrong projection in case labels not in same space View pull request
- sct_extract_metric: Fixed recently-introduced bug related to output results View pull request
ENHANCEMENT
- Few fixes in sct_extract_metric and batch processing outputs View pull request
- sct_dmri_compute_dti: Output tensor eigenvectors View pull request
- Totally pimp the Image Slicer (to act like a sequence, to slice many images), and add unit tests for the slicer View pull request
- Second pass at image refactoring View pull request
This release notably brings a useful feature, which now makes it possible to use single-label with -l flag for registration to the template. This feature was required by the recently-introduced analysis pipeline for multi-parametric data when FOV is systematically centered at a particular disc or mid-vertebral level. View detailed changelog
BUG
sct_register_multimodal: Fixed bug when using partial mask with algo=slicereg View pull request
ENHANCEMENT
sct_propseg: Labels and centerline are now output with correct header if -rescale is used View pull request- Adding a batch size of 4 for all deep learning methods. View pull request
FEATURE
sct_register_to_template: Enable single-label with -l flag View pull request
Major changes to this release include a fix to SCT installation on OSX laptops with non-English encoding language. Another important fix is the inclusion of the link in sct_download_data for downloading the Paris'18 SCT course material. A nice enhancement is the possibility to calculate metrics slice-wise or level-wise in sct_extract_metric. View detailed changelog
View detailed changelog
BUG
- sct_label_vertebrae: Added subcortical colormap for fslview View pull request
- sct_flatten_sagittal: Fixed wrong indexation View pull request
ENHANCEMENT
- sct_deepseg_gm: Lazy loading module: now faster when calling usage View pull request
- sct_propseg: Now possible to rescale data header to be able to segment non-human spinal cord (mice, rats, etc.) View pull request
- sct_deepseg_gm: Adding TTA (test-time augmentation) support for better segmentation results View pull request
- sct_deepseg_gm: Removed restriction on the network input size (small inputs): Fixes bug that appeared when inputting images with small FOV View pull request
- sct_deepseg_sc: Reducing TensorFlow cpp logging verbosity level View pull request
- sct_extract_metric: Now possible to calculate metrics slice-wise or level-wise View pull request
DOCUMENTATION
- Added documentation for installing SCT on Windows using Docker View pull request
- Added information on the README about how to update SCT from git install View pull request
- Updated documentation and added link to the data for the SCT course in Paris View pull request
INSTALLATION
- Use pip install -e spinalcordtoolbox to gain flexibility View pull request
- Local language support (LC_ALL) added to installation& launcher on macOS View pull request
TESTING
- Removed sct_register_graymatter (obsolete old code) from sct_testing functions View pull request
- Implemented multiprocessing and argparse in sct_testing, and other improvements related to Sentry View pull request
This release fixes a few bugs, notably one related to template registration when using disc-based alignment. It also features an improved version of sct_deepseg_sc with the introduction of 3D kernel models, as well as a more accurate segmentation on T1-weighted scans. The main documentation now includes a link to a new collection of repositories: sct-pipeline, which gathers examples of personalized analysis pipelines for processing spinal cord MRI data with SCT. View detailed changelog
BUG
- Skip URL if filename isn't provided by HTTP server; catch anything in URL try loop View pull request
- Fixed registration issue caused by labels far from cord centerline View pull request
- Fixed wrong disc labeling and other minor improvements View pull request
- Added test to make sure not to crop outside of slice range View pull request
- Forcing output type to be float32 View pull request
- Fixed z_centerline_voxel not defined if -no-angle is set to 1 View pull request
ENHANCEMENT
- Adding threshold (or not) option for the sct_deepseg_gm View pull request
- Manual centerline is now output when using viewer View pull request
- Added CNN for centerline detection, brain detection and added possibility for 3d CNN kernel View pull request
- Fixed verbose in QC, integrated coveralls View pull request
- Now possible to specify a vertebral labeling file when using -vert View pull request
DOCUMENTATION
- Added link to github.com/sct-pipeline View pull request
INSTALLATION
- Adapted final verbose if user decided to not modify the .bashrc View pull request
TESTING
- Coveralls added to Travis to prevent build failure View pull request
This release includes: a new example dataset (now includes T2*-w and fMRI data) with an updated batch_processing.sh, a new function to compute MT-saturation effect (sct_compute_mtsat), an improved straightening that can account for inter-vertebral disc positions to be used alongside sct_register_to_template for more accurate registration, and few improvements on sct_pipeline and quality control (QC) report generation. View detailed changelog
BUG
- Fixed sct_pipeline if more than two -p flags are used View pull request
- Fixed re-use of the same figure during QC generation View pull request
- sct_deepseg_sc - Issue when input is .nii instead of .nii.gz View pull request
- Fslview no more called at the end of process if it it deprecated View pull request
- Fixing the TensorFlow installation for some old platforms. View pull request
- Re-ordering of 4th dimension when apply transformation on 4D scans View pull request
- Fix "-split" option issues on sct_image View pull request
ENHANCEMENT
- Updated batch_processing and sct_example_data with new features View pull request
- Various fixes for sct_pipeline View pull request
- sct_pipeline: store metadata in Pickle report View pull request
- Adding volume-wise standardization normalization for the sct_deepseg_gm View pull request
- Make sct_get_centerline robust to intensities with range [0, 1] View pull request
- Improved doc and minor fixes with centerline fitting View pull request
- Make sct_process_segmentation compatible with the new ldisc convention View pull request
- Removed flirt dependency View pull request
- More pessimistic caching of outputs View pull request
- Slice counting fixed View pull request
- output of -display ordered per label value View pull request
- Improvements in straightening and registration to the template View pull request
- The QC report is now a standalone html file. View pull request
- Adding a port option for the qc server View pull request
- Make QC generation opt-in View pull request
- Fixing cropping issue in sct_straighten_spinalcord View pull request
- Set MeanSquares the default metric for sct_fmri_moco View pull request
- Now possible to change data orientation on 4D data View pull request
- Use python concurrent.futures instead of multiprocessing View pull request
FEATURE
- New function to create violin plots from sct_pipeline results View pull request
- Enable input file with label at a specific disc View pull request
- Control the brightness of the image in the GUI. View pull request
- Implements MTsat function View pull request
- Improvements in straightening and registration to the template View pull request
- Integration of SCT into fsleyes UI View pull request
- Add Sentry error reporting View pull request
BUG
- Fix TensorFlow installation on Debian View pull request
- BUG: Fixed a small bug on None condition View pull request
- Fixed missing output View pull request
- Bug fix and various improvements View pull request
- Now working for 2d data View pull request
- Fix Timer with progress View pull request
- BUG: concat_transfo: fixed wrong catch of dimension View pull request
- reinstall only current numpy version View pull request
- Enable the calculation of spinal cord shape at the edge of the image View pull request
- Disabling rotation in register to template View pull request
ENHANCEMENT
- Adding minimal Dockerfile for SCT. View pull request
- Bug fix and various improvements View pull request
- Find mirror servers in case OSF is not accessible View pull request
- Now supports fsleyes when displaying viewer syntax at the end of a process View pull request
FEATURE
- sct_deepseg_sc implementation View pull request
- sct_deepseg_gm implementation View pull request
TESTING
- Fixed minor verbose issues during testing View pull request
BUG
- Fix errors in create_atlas.m View pull request
- Fix a regression bug. View pull request
- Used the absolute path to create the temporary label file in propseg View pull request
- Fixed: Optic is used by default if -init-mask is used with external file provided View pull request
- Fixed global dependency in sct_process_segmentation call View pull request
- Fixed z-regularization for slicereg View pull request
ENHANCEMENT
- Fixed: Raise in sct.run in bad order. Also added specific sct errors View pull request
- More improvements to the viewer View pull request
- Refactored WM atlas creation pipeline and improved documentation View pull request
- Option to install SCT in development mode View pull request
- Added key bindings to the undo, save and help actions. View pull request
- Introduced the zoom functionality to the anatomical canvas View pull request
- Improvements on centerline for template generation View pull request
- Major refactoring of testing framework View pull request
FEATURE
- Improvement of sct_analyze_lesions: compute percentage of a given tract occupied by lesions View pull request
- sct_get_centerline: new manual feature View pull request
- sct_detect_pmj: new_feature View pull request
TESTING
- Major refactoring of testing framework View pull request
BUG
- Added try/except for QC report View pull request
- Conversion issue for float32 images with large dynamic View pull request
- (Partly-)Fixed bug related to memory issue with diagonalization View pull request
- DEV: fixed bug on centerline when referencing to the PMJ View pull request
ENHANCEMENT
- Now possible to input single label at disc (instead of mid-body) View pull request
- Now using N-1 instead of N as denominator for computing the STD. View pull request
FEATURE
- Function to analyze lesions #1351 View pull request
BUG
- The params attributes are initialized to the type integer View pull request
- Fixing stdout issue on sct_testing View pull request
- Changed destination image for concatenation of inverse warping field View pull request
- crashes if apply transfo on 4d images View pull request
- Allow the -winv parameter to write a file to disk View pull request
- Change import path of resample View pull request
- Precision error while calculating Dice coefficient #1098 View pull request
ENHANCEMENT
- Enables to set Gaussian weighting of mutual information for finding C2-C3 disk View pull request
- Adapt concat and apply transfo to work on 2d images View pull request
- Fixed small issues in pipeline View pull request
- Use custom template for sct_register_graymatter View pull request
- compute_ernst_angle: set the parameter t1 default value to optional value of 850ms View pull request
- Improvements on centerline and template generation View pull request
FEATURE
- NEW: dmri_display_bvecs: new function to display bvecs View pull request
- Function to extract texture features #1350 View pull request
TESTING
- Various fixes to pipeline and testing View pull request
- New test for sct_label_utils compatible with sct_pipeline View pull request
DOCUMENTATION
- Changed default values and clarified doc View pull request
BUG
- Catch the OSError exception thrown when the git command is missing View pull request
- BUG: register_multimodal: fixed typo when calling isct_antsRegistration View pull request
- BUG: fix bug when slice is empty View pull request
- Ignore using user packages when install with conda and pip View pull request
- Fix referential for JIM centerline View pull request
- image/pad: now copy input data type (fixes issue 1362) View pull request
- Use a pythonic way to compare a variable as None View pull request
- The init-mask accepts "viewer" as a value View pull request
- Fixed unassigned variable in case -z or -vert is not used View pull request
ENHANCEMENT
- Restrict deformation for ANTs algo View pull request
- Made error message more explicit if crash occurs View pull request
- Insert previous and next buttons in the qc reports page View pull request
- integrate new class for multiple stdout inside sct_check_dependencies View pull request
DOCUMENTATION
- Update README.md View pull request
INSTALLATION
- Ignore using user packages when install with conda and pip View pull request
- Update sct testing data View pull request
- Added the dependency psutil in the conda requirements View pull request
- Added egg files in the list of gitignore View pull request
BUG
- Force numpy 1.12.1 on osx and linux View pull request
- Use a different function to identify if a file exists View pull request
- Fixing an issue introduced with the sct_get_centerline. View pull request
ENHANCEMENT
- Binarize GM seg after warping back result to original space View pull request
- Generation of centerline as ROI View pull request
FEATURE
- Introduce a pipeline to use the HPC architecture View pull request
BUG
- Normalize the init value to between 0 and 1 for propseg View pull request
- Moved the QC assets into the spinalcordtoolbox package View pull request
- Improved the formatting of the changelog generator View pull request
- Show remaining time status for downloads View pull request
ENHANCEMENT
- Added the command parameter
-noqcView pull request - Add dimension sanity checking for input file padding op View pull request
FEATURE
- Introducing spinal cord shape symmetry View pull request
TESTING
- Validate the function name in sct_testing View pull request
- Fix regression bug in sct_testing View pull request
BUG
- Fixes case if data image, segmentation and labels are not in the same space View pull request
- Fix the handling of the path of the QC report. View pull request
- Change the format of the SCT version. View pull request
- changed the DISPLAY variable due to conflicts with FSLView in batch_processing.sh View pull request
INSTALLATION
- Added course_hawaii17 into the list of available dataset from sct_download_data View pull request
- Incorrect variable when installing SCT in a different directory View pull request
DOCUMENTATION
- Added description with examples in the register_to_template command (#1262) View pull request
- Fixed typo in register_multimodal command View pull request
BUG
- Force the SCT environment to use only the python modules installed by SCT View pull request
- Fixing disabling options on straightening View pull request
- Fixed tSNR computation of the mean and std of the input image View pull request
- Increased the data type size from the default int16 to int32 to avoid overflow issues in sct_process_segmentation View pull request
- Fixed data type issue in sct_process_segmentation View pull request
ENHANCEMENT
- Improvements to denoising on sct_segment_graymatter View pull request
- Extend the functionality of sct_viewer View pull request
- Add OptiC for improved spinal cord detection View pull request
- Introduction spinalcordtoolbox python setup file View pull request
FEATURE
- Add option -rms to perform root mean square (instead of mean) in sct_maths View pull request
- Introduce QC report generation View pull request
- Introduce the QC html viewer View pull request
TESTING
- Introduce the QC html viewer View pull request
- Introduce python package configuration file (setup.cfg) View pull request
- Merge multiple source images onto destination space. View pull request
- Modifying the type of coordinates for vertebral matching View pull request
- Removing discontinuities at edges on segmentation View pull request
- BUG: computing centreline using physical coordinates instead of voxel… View pull request
- Fix issue #1172: -vertfile as an optional parameter View pull request
- Improvements to the viewer of sct_propseg View pull request
- Removed confusion with command variables when using PropSeg viewer View pull request
- Patch sct_register_to_template with -ref subject View pull request
- zero voxels no more included when computing MI + new flag to compute normalized MI View pull request
- Changed default threshold_distance from 2.5 to 10 to avoid edge effect View pull request
- Adapt sct_create_mask and sct_label_utils to 2D data View pull request
- Improvements to the viewer of sct_propseg View pull request
- OPT: display mean and std instead of mean twice View pull request
- BUG: install_sct: fixed PATH issue (#1153): closed at 2017-02-08 View pull request
- BUG: compute_snr: fixed variable name: closed at 2017-02-03 View pull request
- Changed the algorithm to fetch the download filename: closed at 2017-02-03 View pull request
- Copy header of input file to ensure qform is unchanged: closed at 2017-01-31 View pull request
- zero voxels no more included when computing MI + new flag to compute normalized MI: closed at 2017-02-01 View pull request
- Downloading the binaries using the python module instead of CURL: closed at 2017-01-30 View pull request
- [sct_segment_graymatter] correct background value: closed at 2017-01-31 View pull request
- Fixing indexes issue on Travis OSX: closed at 2017-01-17 View pull request
- REF: display spinal cord length when required (full spinal cord): closed at 2017-01-17 View pull request
- Adding rules for in-segmentation errors: closed at 2017-01-17 View pull request
- Generate a changelog from GitHub: closed at 2017-02-10 View pull request
- OPT: maths: visu only produced if verbose=2: closed at 2017-02-02 View pull request
- Add message to user when spinal cord is not detected and verbose improvement for testing: closed at 2017-02-01 View pull request
- Display results of isct_test_function: closed at 2017-01-20 View pull request
- BUG: sct_process_segmentation display spinal cord length when required (full spinal cord) (#1112)
- BUG: sct_propseg Adding rules for in-segmentation errors (#1110)
- BUG: PAM50: probabilist templates of WM and GM not sum to 1 (#411)
- BUG: sct_propseg: fixed edge issue (#1074)
- BUG: sct_label_vertebrae: fixed temporary folder not created (#1083)
- BUG: isct_test_function: fixed temp folder of subject being created inside test folder of another subject (#1084)
- BUG: sct_apply_transfo: fixed TR field on NIFTI is lost (#1013)
- BUG: sct_register_graymatter: fixed empty inverse warping field (#1068)
- OPT: sct_label_vertebrae: now outputing verbose=2 pics in ofolder (#1094)
- OPT: sct_straighten_spinalcord: fixed Reduce required RAM (#979)
- OPT: sct_straighten_spinalcord: removes accuracy computation by default (#1075)
- OPT: sct_propseg: improve robustness towards exception (#207)
- OPT: isct_test_function: send email when finished (#1081)
- OPT: isct_test_function: removed color tags on log entries (#1035)
- NEW: PAM50 template now used as the default template
- NEW: sct_compute_snr: compute SNR using several methods (Dietrich et al. 2007)
- NEW: sct_propseg: now accepts a correction solution for sct_propseg in case of missing CSF/SC contrast and/or artefacts (see issue #664 for details)
- NEW: sct_propseg: added flag to open a viewer for initializing spinal cord segmentation by manually providing a few points (issue #741)
- NEW: install_sct: new installer, which downloads the necessary data (i.e., lighter package).
- NEW: SCT now includes its own python (from miniconda), which simplifies the installation and allows users to have another Python installed without generating conflicts.
- NEW: sct_dmri_create_noisemask: Identification and estimation of noise in the diffusion signal, implemented by the Dipy software project (http://nipy.org/dipy/), based on the PIESNO method
- NEW: sct_register_graymatter: Multi-label registration that accounts for gray matter shape.
- NEW: sct_register_multimodal: features two new transformations: centermassrot and columnwise.
- NEW: sct_register_multimodal: flag smoothWarpXY: regularization of warping field (only for algo=columnwize)
- NEW: sct_register_multimodal: flag pca_eigenratio_th: Min ratio between the two eigenvalues for PCA-based angular adjustment (only for algo=centermassrot).
- NEW: sct_create_mask: now compatible with 2D data (#1066)
- NEW: sct_maths: computes mutual information and cross-correlation between images (#1054)
- BUG: sct_straighten_spinalcord: Fixed #917, #924, #1063
- BUG: Fixed issues #715, #719
- BUG: sct_propseg: fixed issues #147, #242, #309, #376, #501, #544, #674, #680
- BUG: sct_segment_graymatter: fixed issues #782, #813, #815
- BUG: sct_register_graymatter: fixed issue #1068
- BUG: Fixed incompatibility with CENTOS 6.X (issue #776)
- BUG: Binaries now hosted on Gihub for accessibility from China (#927)
- BUG: sct_resample: Fixed slight image shift caused by resampling (#612)
- OPT: sct_check_dependencies: Made test more sentitive to OS incompatibilities (issue #771)
- OPT: sct_register_multimodal: major changes. Simplified flags. Fixed issues #350, #404, #414, #499, #650, #735, #737, #749, #807, #818, #1033, #1034
- OPT: sct_register_to_template: now uses slicewise rigid transfo at first step (instead of slicereg), which improves accuracy (issue #666)
- OPT: sct_register_to_template: added contrast for registration: t2s
- OPT: sct_label_vertebrae: now fully automatic (although unstable-- work in progress).
- OPT: sct_testing: added integrity testing for CSA computation (#1031)
- REF: sct_testing: sct_testing_data is now hosted on GitHub-release for better tracking and across-version compatibility.
- BUG: sct_process_segmentation: Fixed issue related to calculation of CSA (#1022)
- BUG: sct_label_vertebrae: Fixed Vertebral labeling removes first vertebrae in the labelled segmentation (#700)
- OPT: sct_register_multimodal: Now possible to input initial warping field (#1049)
- OPT: sct_register_multimodal: Added feature to be able to input two pairs of label image for estimating affine/rigid/nonrigid transformation (#661)
- OPT: sct_extract_metric: Added weighted-Maximum a posteriori extraction method (#1018)
- OPT: Remove color tags on log entries (#1035)
- NEW: sct_extract_metric: method "max" to extract CSA value form interpolated volume (e.g. PAM50 space) without partial volume bias
- INST: Fixed #992, #1004, #1008, #1012
- OPT: Fixed #875
- INST: Fixed #1007, #1009
- BUG: Fixed #870, #898, #859, #871, #1005, #750, #444, #878, #1000
- INST: Fixed issue with matplotlib version 1.5.3
- BUG: Fixed #984, #983, #954, #978, #987, #938, #964, #638, #969, #922, #855
- OPT: sct_register_to_template: added a flag "-ref" to be able to register to anisotropic data
- BUG: Fixed #994, #989, #988, #976, #968
- BUG: sct_straighten_spinalcord: fixed instabilities related to generation of labels (issue #722)
- OPT: sct_dmri_moco: added flag "-bvalmin" to specify b=0 threshold and improved reading of bval file.
- BUG: sct_dmri_moco: fixed bug related to the use of mask
- BUG: sct_dmri_moco: fixed bug in the algorithm (iterative average of target DWI volume)
- BUG: Fixed major issue during installation (issue #708)
- BUG: sct_process_segmentation: fixed bug occuring with small FOV (issue #706)
- BUG: sct_resample: fixed issue #691
- OPT: sct_segment_graymatter: improved robustness of normalization
- OPT: sct_process_segmentation: default parameter does not smooth CSA results anymore
- NEW: sct_testing: test SCT functions and their integrity
- NEW: sct_maths: performs basic operations on images. Similar to fslmaths.
- NEW: sct_get_centerline -method auto: uses advanced image processing methods for finding the spinal cord centerline automatically on any type of contrast. This script should be followed by sct_propseg for finer cord segmentation.
- NEW: sct_label_vertebrae: can automatically label vertebral levels given an anatomical scan, a centerline and few prior info.
- NEW: sct_segment_graymatter: segment spinal cord gray matter using multi-atlas approach from Asman et al.
- NEW: sct_process_segmentation: feature to estimate CSA based on labels
- NEW: sct_label_utils: new functionality for creating labels based on vertebral labeling
- NEW: added "-qc" flag to some functions to output png images for quality control.
- BUG: install_patch: now possible to install as non-admin (issues #380, #434)
- BUG: sct_extract_metric: fix the case when averaging labels from different clusters with method map
- INST: no more dependence with FSL
- INST: no more dependence with c3d
- OPT: sct_straighten_spinalcord: improved accuracy (issues #371, #425, #452, #472)
- OPT: sct_registration_to_template: improved accuracy
- REF: harmonization of flags. Most flags from v2.0 still work but a message of deprecation is sent.
- sct_process_segmentation: fixed issue with computation of volume based on vertebral level (slice selection now using centerline)
- fixed compatibility with new PAM50 template
- harmonized flags
- sct_process_segmentation: now computes volume
- BUG: sct_process_segmentation: fixed bug of output file location (issue #395)
- BUG: sct_process_segmentation: fixed error when calculating CSA (issue #388)
- BUG: sct_process_segmentation: fixed error when calculating CSA (issue #388)
- BUG: Hanning smoothing: fixed error that occurred when window size was larger than data (issue #390)
- OPT: sct_check_dependencies: now checks if git is installed
- OPT: simplified batch_processing.sh
- BUG: sct_register_to_template: fixed issue related to appearance of two overlapped templates in some cases (issue #367)
- BUG: sct_register_to_template: now all input data are resampled to 1mm iso to avoid label mismatch (issue #368)
- BUG: sct_resample: fixed bug when user specified output file
- OPT: sct_create_mask: improved speed
- BUG: sct_fmri_compute_tsnr: fixed issue when input path includes folder
- BUG: sct_orientation: now possibility to change orientation even if no qform in header (issue #360)
- BUG: msct_smooth: fixed error with small Hanning window (issue #363)
- BUG: sct_straighten_spinalcord: fixed issue with relative path (issue #365)
- NEW: sct_label_utils: added new function to transform group of labels into discrete label points
- NEW: sct_orientation: added a tool to fix wrong orientation of an image (issue #366)
- OPT: sct_register_to_template: twice as fast! (issue #343)
- BUG: sct_extract_metric: MAP method did not scale properly with the data. Now fixed (issue #348)
- BUG: fixed issue with parser when typing a command to see usage (it crashed)
- NEW: sct_fmri_compute_tsnr: new function to compute TSNR from fMRI data (performs moco before)
- OPT: sct_straighten_spinalcord: now MUCH faster and more accurate (issue #240)
- OPT: sct_register_to_template: allows more flexibility by allowing multiple steps for registration (flag -p).
- N.B. flag "-m" has been replaced by "-s"
- OPT: sct_register_multimodal: allows more flexibility by imposing only one stage. Several stages can be run sequentially and then transformations can be concatenated.
- N.B. flags "-s" and "-t" were replaced with "-iseg" and "-dseg" respectively
- OPT: sct_extract_metric:
- new methods for extraction: maximum likelihood and maximum a posteriori, which take into account partial volume effect
- now possible to specify global regions for extraction with flag -l: wm, gm, sc
- now possible to include a bunch of labels using ":". Example: 2:29
- NEW: sct_get_centerline_from_labels: obtain a centerline using a combination of labels and/or segmentations
- N.B. sct_get_centerline was renamed for sct_get_centerline_automatic
- NEW: sct_compute_ernst_angle: new script to compute and display Ernst angle depending on T1 and TR
- OPT: sct_process_segmentation:
- can compute average CSA across vertebral levels or slices
- can compute length of segmentation
- can compute CSA on non-binary images such as probabilistic gray/white matter maps
- N.B. process names were simplified to: "csa", "length" and "centerline"
- OPT: sct_crop_image: now possible to crop an image based on a reference space
- OPT: new WM atlas: added gray matter and CSF for computing partial volume
- OPT: now use all available cores for ANTs and adjust variable when running dmri_moco (issue #238)
- INST: new installer in python, simpler to use and check for latest patches
- REF: msct_parser: new parser that generate documentation/usage
- REF: msct_image, sct_label_utils: smoothly converting the toolbox to objet-oriented, some scripts can be used as python module
- BUG: sct_dmri_moco: fixed crash when using mask (issue # 245)
- OPT: sct_create_mask: (1) updated usage (size in vox instead of mm), (2) fixed minor issues related to mask size.
- INST: links are now created during installation of release or patch (issue ).
- FIX: updated ANTs binaries for compatibility with GLIBC_2.13 (issue: https://sourceforge.net/p/spinalcordtoolbox/discussion/help/thread/e00b2aeb/)
- NEW: sct_crop: function to quickly crop an image.
- NEW: sct_extract_metric (replaces the old sct_estimate_MAP_tracts.py). New functionalities added (maximum likelihood estimation and tract grouping). More flexible with label files.
- NEW: sct_convert_mnc2nii
- NEW: sct_create_mask: create mask of different shapes (cylinder, box, gaussian). Useful for moco.
- NEW: sct_fmri_moco: motion correction function for fMRI data. Uses regularization along z.
- NEW: sct_compute_mtr: compute MTR
- NEW: sct_otsu: OTSU segmentation (usefull for DWI data)
- NEW: sct_resample: quick upsample/downsample 3D or 4D data
- NEW: sct_segment_greymatter: function to segment the grey matter by warping that one from the atlas
- OPT: sct_orientation can now be applied to 4d data
- OPT: sct_register_multimodal now using the new antsSliceReg method that regularizes along z.
- OPT: new version of the white matter atlas: more accurate, deformation accounting for internal structure (use BSplineSyN instead of SyN).
- OPT: sct_dmri_moco now using the new antsSliceReg method that regularizes along z.
- OPT: removed all .py extensions for callable functions (created links)
- OPT: sct_label_utils: now possible to create labels. Also added other useful features.
- INST: now possible to specify installation path for the toolbox
- INST: conda dependences are now automatically installed by the installer.
- INST: added pillow (fixed issue #117)
- INST: "getting started" now provided via example commands in batch_processing.sh
- REF: sct_straighten_spinalcord (fixed issues #56, #116)
- TEST: major changes on the testing framework for better modularity with Travis. Now using separate small dataset.
- BUG: fixed bug in sct_process_segmentation.py related to import of scipy.misc imsave,imread in miniconda distrib (issue #62)
- BUG: fixed bug in sct_process_segmentation.py related to import of PIL/Pillow module (issue #58)
- OPT: sct_register_multimodal now working for images with non-axial orientation (issue #59)
- OPT: sct_register_straight_spinalcord_to_template has now been replaced by sct_register_multimodal in sct_register_to_template.
- OPT: major improvements for sct_dmri_moco, including spline regularization, eddy correction, group-wise registration, gaussian mask.
- OPT: sct_check_dependencies.py can now output log file and do extensive tests (type -h for more info)
- NEW: sct_apply_transfo.py: apply warping field (wrapper to ANTs WarpImageMultiTransform)
- NEW: sct_concat_transfo.py: concatenate warping fields (wrapper to ANTs ComposeMultiTransform)
- NEW: batch_processing.sh: example batch for processing multi-parametric data
- NEW: virtual machine
- BUG: fixed sct_check_dependencies for Linux
- BUG: fix VM failure of sct_register_to_template (issue #41)
- OPT: sct_register_to_template.py now registers the straight spinal cord to the template using sct_register_multimodal.py, which uses the spinal cord segmentation for more accurate results.
- INST: toolbox now requires matplotlib
- first public release!
- NEW: dMRI moco
- INST: libraries are now statically compiled
- OPT: propseg: now results are reproducible (i.e. removed pseudo-randomization)
- Debian + OSX binaries
- BUG: fixed registration2template issue when labels were larger than 9
- BUG: fixed bug on PropSeg when the image contains a lot of null slices
- INST: now installer write on bashrc and links bash_profile to bashrc
- BUG: removed random parts in PropSeg
- now possible to get both template2EPI and EPI2template warping fields
- fixed major bug in registration (labels were cropped)
- NEW: probabilistic location of spinal levels
- NEW: binaries for Debian/Ubuntu
- NEW: installer for ANTs (currently only for OSX)
- fixed bugs
- major changes in sct_register_multimodal
- fixed bugs
- NEW: nonlocal means denoising filter
- NEW: sct_smooth_spinalcord --> smoothing along centerline
- fixed bugs
- first beta version!