Changelog

5.0.0 (2020-11-07)

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FEATURE

• sct_get_centerline,sct_qc: Implement QC sct_get_centerline. View pull request

• sct_run_batch: Disabling progress bars. View pull request

• sct_label_utils,sct_qc: Implemented QC report for sct_label_utils. View pull request

BUG

• Logging and printing fixes. View pull request

• Restore subpackage module imports to fix test errors. View pull request

• Fix incorrect checking of input arguments. View pull request

• sct_register_to_template: sct_register_to_template: Fix ‘%’ in argparse iCloud help links. View pull request

INSTALLATION

• sct_utils: Explicit listing of console scripts. View pull request

• Retrieve data bundles from their new location. View pull request

DOCUMENTATION

• Update sct_extract_metric help to fix RTD error + fix outdated usage. View pull request

• Add “Segmentation” tutorial to RTD that mirrors SCT course contents. View pull request

• fix doc build warnings + associated bug. View pull request

• Update Win10 WSL installation information (Move from Wiki to RTD, update recommendations for FSLEyes/WSL1). View pull request

• Update LICENSE to LGPLv3. View pull request

• Automatically show defaults in argparse help descriptions. View pull request

ENHANCEMENT

• sct_extract_metric: Introduce flag to list labels. View pull request

• sct_register_to_template: Fixes inconsistencies between PAM50 levels and cord. View pull request

• Use SystemExit not sys.exit & only on error paths.. View pull request

• fsleyes: allow user to specify output folder. View pull request

• sct_image: sct_image: -copy-header should use -o as output file. View pull request

• sct_concat_transfo: Deprecate sct_concat_transfo + refactor callers. View pull request

• sct_maths: sct_maths: Convert usage of convert_list_str to use list_type. View pull request

• sct_run_batch: Prevent crash if folder already exists. View pull request

• msct_parser: Convert 11-20 out of 20 remaining scripts from msct_parser to argparse. View pull request

• sct_run_batch: Fix thread reporting, early termination, and indentation error in sct_run_batch. View pull request

• msct_parser: Convert 1-10 out of 20 remaining scripts from msct_parser to argparse. View pull request

• sct_apply_transfo: Clarified cropping strategy for sct_apply_transfo; remove warning. View pull request

• sct_run_batch: Various improvements. View pull request

• sct_run_batch: Introduced variable PATH_DATA_PROCESSED. View pull request

• sct_deepseg: Accommodate a cascade of deep learning models. View pull request

• Improvements for the FSLeyes plugin. View pull request

• sct_run_batch: Various improvements: create log, send email, config file, include/exclude list of subjects. View pull request

REFACTORING

• msct_parser: Remove msct_parser and clean up remaning usage. View pull request

• Convert argparse ‘0’/’1’ options to be typed as ints rather than strings. View pull request

4.3 (2020-06-11)

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BUG

• sct_label_vertebrae: Fixed -initlabel problem with file naming. View pull request

• sct_utils: Fix and move send_email. View pull request

• sct_qc: Fix out of order plots. View pull request

• sct_label_utils: sagittal dialog: fixes error when trying to access out of bound slice. View pull request

• sct_register_multimodal: Fixed forgot to reorient mask. View pull request

• sct_label_vertebrae: -initz flag and label value correction. View pull request

• sct_qc: Test for parallel qc crash. View pull request

• Replace parser.usage.generate with parser.error. View pull request

ENHANCEMENT

• sct_download_data: Moved sct_download_data functions to new download module. View pull request

• SCT logo fix in FSLeyes. View pull request

• sct_run_batch: Flag -s added to force sequential analysis even if GNU parallel is installed. View pull request

FEATURE

• Added useful formatting to compare SCT versions; introduced sct_version. View pull request

• sct_get_centerline: Fit centerline across all slices with input segmentation. View pull request

• sct_deepseg,sct_download_data: Centralized all deep learning segmentation tasks with new function “sct_deepseg” and refactored sct_download_data. View pull request

• sct_dmri_moco,sct_fmri_moco: Now possible to use soft mask, bug fixes and various improvements. View pull request

• parameters_example.sh: Now defined a relative PATH_PARENT. View pull request

• sct_maths: Enable 2D kernel for morpho math operations and various improvements. View pull request

• sct_apply_transfo: Fixed compatibility between SCT/ANTs and FSL warping fields. View pull request

DOCUMENTATION

• Fix argparse linewrap for R| strings. View pull request

• Added video recording of the London 2020 course. View pull request

• Update badge for discourse forum. View pull request

• sct_dmri_concat_b0_and_dwi: Clarified documentation. View pull request

• Added tutorial to install SCT with WSL for Windows users. View pull request

• Fixed README forum link. View pull request

INSTALLATION

• Drop support for 2014-era Linux.. View pull request

• Minimal Torch install.. View pull request

• sct_dmri_moco,sct_fmri_moco: Updated ANTs binaries to solve slow processing in some systems. View pull request

• Downgraded TensorFlow to 1.5 to fix AVX incompatibility. View pull request

TESTING

• Added CI for Windows Subsystem for Linux (WSL). View pull request

• sct_get_centerline: Relax test tolerance for centerline polyfit. View pull request

• Add polynomial function to dummy_segmentation. View pull request

• create_test_data: move to spinalcordtoolbox.testing. View pull request

4.2.2 (2020-02-28)

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BUG

• sct_maths: Fixed missing type when using erode feature. View pull request

• sct_crop_image: Fixed flag -b crops instead of masking. View pull request

• sct_crop_image: Fixed problem with parameters xmax, ymax and zmax. View pull request

• sct_deepseg_sc,sct_utils: Check if input data is 3D or 2D. View pull request

ENHANCEMENT

• sct_deepseg_gm,sct_deepseg_lesion,sct_deepseg_sc: build(deps): bump tensorflow from 2.0.0 to 2.0.1. View pull request

• Added more functions to the FSLeyes plugin. View pull request

DOCUMENTATION

• sct_qc: Fixed QC display syntax for Docker users. View pull request

4.2.1 (2020-01-14)

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BUG

• sct_warp_template: Fixed generation of QC report. View pull request

• sct_register_multimodal: Fixed bug related to missing output file. View pull request

ENHANCEMENT

• sct_utils: Changed default open command for Linux. View pull request

• sct_deepseg_sc,sct_label_vertebrae: Better error handling if installation files are missing and clarified help. View pull request

INSTALLATION

• Added gcc as installation pre-requisite with useful instructions. View pull request

4.2.0 (2019-12-19)

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ENHANCEMENT

• sct_register_multimodal,sct_register_to_template: New method for detecting rotation in centermassrot. View pull request

FEATURE

• sct_register_to_template: Spinal-level-based registration to the PAM50. WARNING: Breaks compatibility with previous versions of SCT. View pull request

DOCUMENTATION

• Added info for running SCT via Vbox. View pull request

INSTALLATION

• Now using requirements-freeze.txt for installing stable releases. View pull request

• install/sct_changelog: Fixed bug when fetching previous release tag. View pull request

• Removed Darwin=15 case in requirements.txt and added OS checks during installation. View pull request

4.1.1 (2019-11-28)

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BUG

• sct_register_to_template: Fixed cropping of registered image. View pull request

• sct_run_batch: Fixed issue when passing absolute path to script. View pull request

FEATURE

• sct_apply_transfo: Added an option for keypoints transformation. View pull request

• sct_label_utils: Now possible to add existing label from an external file in the create-viewer option. View pull request

DOCUMENTATION

• README: Added link to Youtube tutorials. View pull request

INSTALLATION

• sct_viewer: PyQt5 version downgrade to fix GUI on Debian 8.11 distros. View pull request

• sct_check_dependencies: Increased sensitivity of dependency testing. View pull request

4.1.0 (2019-10-26)

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BUG

• sct_compute_mtr: Fixed aberrant mtr values. View pull request

• sct_process_segmentation: Fixed wrong orientation with new version of scikit-image. View pull request

• sct_maths: Fixed deprecation with adaptative thresholding. WARNING: Breaks compatibility with previous versions of SCT. View pull request

• sct_deepseg_sc: Fixed segmentation issue that mostly appeared on DWI data. WARNING: Breaks compatibility with previous versions of SCT. View pull request

• sct_qc,sct_resample: QC report: Fixed shift along slice direction between image and overlay. View pull request

• sct_straighten_spinalcord: Fixed shape mismatch during straightening. View pull request

• sct_denoising_onlm: Fix index error and display fsleyes command. View pull request

ENHANCEMENT

• sct_resample: Raise error if trying to resampling to size zero. View pull request

• sct_deepseg_sc: Fix deepseg threshold (again). View pull request

• sct_deepseg_sc: Fine-adjustment of threshold for binarization of soft segmentation. View pull request

• sct_qc: Fixed up/down dysfunction in the qc report . View pull request

• sct_crop_image: Improved CLI, fixed bug with the GUI and refactored into module. WARNING: Breaks compatibility with previous versions of SCT. View pull request

• sct_deepseg_sc: Remove isolated voxels at the edge of the output segmentation. View pull request

• sct_download_data: Check if folder already exists by checking its actual name, not the name of the entry to -d flag. View pull request

FEATURE

• sct_qc: Added button to toggle overlay and removed automatic fading. View pull request

• sct_dmri_concat_b0_and_dwi: New script to concatenate b0 and dwi data. View pull request

• sct_process_segmentation: Compute cord length. View pull request

DOCUMENTATION

• Better management of CLI syntax in case mandatory arguments are missing. View pull request

INSTALLATION

• sct_download_data: Fixed issue that appeared when trying to remove temporary folder from different file systems. View pull request

4.0.2 (2019-09-04)

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BUG

• sct_straighten_spinalcord: Fixed wrong input arguments. View pull request

• sct_fmri_moco: Replaced sct.mv with shutil.copyfile for tmp space issue. View pull request

4.0.1 (2019-08-17)

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BUG

• sct_dmri_compute_dti: Fixed flag ‘-evecs’ not detecting input as of type int. View pull request

• sct_image: Fixed -setorient-data giving wrong results. View pull request

• sct_image: Proper handling of int arguments contained in list type input. View pull request

• sct_process_segmentation: Fixed wrong morphometric measures with anisotropic in-plane resolution. View pull request

• Change canvas axes for image placement.. View pull request

ENHANCEMENT

• sct_process_segmentation: Corrected wrong slice information on QC output. View pull request

• sct_apply_transfo: Fixed q/sform on transformed image. View pull request

INSTALLATION

• sct_resample: Dropped dependency to nipy. WARNING: Breaks compatibility with previous versions of SCT. View pull request

• Check if gcc is installed. View pull request

• Modify bashrc on sudo. View pull request

4.0.0 (2019-08-04)

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BUG

• sct_crop_image: Fixed bug when using GUI (flag -g). View pull request

• sct_label_vertebrae: Fixed misplaced label in non-RPI data for initializing vertebral labeling. View pull request

• 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

• batch_processing.sh: Replaced propseg by deepseg_sc. View pull request

• batch_processing.sh: QC report is now generated locally. View pull request

• msct_parser: Conversion from msct_parser to argparse. View pull request

• sct_qc: Allow the possibility to discard column of choice on the output html QC report. View pull request

• sct_process_segmentation,sct_straighten_spinalcord: Improve quality of straightening. View pull request

• sct_deepseg_lesion,sct_deepseg_sc: Output segmentation in uint8 when input is float. View pull request

• sct_qc: Added automatic data sorting in the QC report. View pull request

• sct_fmri_moco: Enabling the extraction of fMRI motion correction parameters. View pull request

• sct_qc,sct_resample: Fixed resampling method with reference image and improved speed for generating QC report. View pull request

• sct_compute_mtr: Added output file and/or folder flag. View pull request

• sct_compute_snr: Make consistent STD calculation between sct_fmri_compute_tsnr and sct_compute_snr. View pull request

• 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: Add CSA results on QC report . View pull request

• sct_extract_metric: Added flag to combine all labels. View pull request

• sct_dmri_compute_dti: Output DTI Eigenvalues. View pull request

• 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 documentation on how to create vertebral and disc labels. View pull request

• sct_changelog: Few improvements on automatic Changelog generation. View pull request

INSTALLATION

• Fixed compatibility with OSX 10.11 (El Capitan). View pull request

• Fixed Keras/Tensorflow compatibility with CentOS 7 by downgrading to Python 3.6. View pull request

• Using Python 3.x 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

• Travis: Adding distribs and displaying allow_failures. View pull request

• sct_deepseg_lesion,sct_deepseg_sc: Added new unit tests. View pull request

v3.2.7 (2018-10-29)

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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

v3.2.6 (2018-10-16)

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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

v3.2.4 (2018-08-24)

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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

v3.2.3 (2018-07-21)

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

v3.2.2 (2018-07-08)

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

3.2.1 (2018-06-12)

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

3.2.0 (2018-05-29)

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

3.1.1 (2018-02-16)

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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

v3.1.0 (2017-10-27)

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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

v3.0.8 (2017-09-13)

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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

v3.0.7 (2017-08-02)

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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

v3.0.6 (2017-07-04)

View detailed changelog

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

v3.0.5 (2017-06-09)

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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

v3.0.4 (2017-05-19)

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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 -noqc View 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

v3.0.3 (2017-04-26)

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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

v3.0.2 (2017-04-20)

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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

v3.0.1 (2017-03-22)

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FEATURE

• Merge multiple source images onto destination space. View pull request

v3.0.0 (2017-03-15)

View detailed changelog

BUG

• 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

ENHANCEMENT

• 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

TESTING

• OPT: display mean and std instead of mean twice View pull request

3.0_beta32 (2017-02-10)

View detailed changelog

BUG

• 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

ENHANCEMENT

• 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

TESTING

• 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

3.0_beta31 (2017-01-16)

• 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)

3.0_beta29 (2016-12-13)

• 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.

3.0_beta28 (2016-11-25)

• 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)

3.0_beta27 (2016-10-23)

• NEW: sct_extract_metric: method “max” to extract CSA value form interpolated volume (e.g. PAM50 space) without partial volume bias

3.0_beta26 (2016-10-05)

• INST: Fixed #992, #1004, #1008, #1012

3.0_beta25 (2016-09-30)

• OPT: Fixed #875

• INST: Fixed #1007, #1009

3.0_beta24 (2016-09-28)

• BUG: Fixed #870, #898, #859, #871, #1005, #750, #444, #878, #1000

• INST: Fixed issue with matplotlib version 1.5.3

3.0_beta23 (2016-09-18)

• 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

3.0_beta22 (2016-09-09)

• BUG: Fixed #994, #989, #988, #976, #968

2.2.3 (2016-02-04)

• BUG: sct_straighten_spinalcord: fixed instabilities related to generation of labels (issue #722)

2.2.2 (2016-01-31)

• OPT: sct_dmri_moco: added flag “-bvalmin” to specify b=0 threshold and improved reading of bval file.

2.2.1 (2016-01-29)

• 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)

2.2 (2016-01-23)

• BUG: Fixed major issue during installation (issue #708)

• BUG: sct_process_segmentation: fixed bug occuring with small FOV (issue #706)

2.1.1 (2016-01-15)

• 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

2.1 (2015-12-01)

• 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.

2.1_beta21 (2015-11-30)

• sct_process_segmentation: fixed issue with computation of volume based on vertebral level (slice selection now using centerline)

2.1_beta20 (2015-11-30)

• fixed compatibility with new PAM50 template

2.1_beta19 (2015-11-25)

• harmonized flags

• sct_process_segmentation: now computes volume

2.0.6 (2015-06-30)

• BUG: sct_process_segmentation: fixed bug of output file location (issue #395)

2.0.5 (2015-06-10)

• BUG: sct_process_segmentation: fixed error when calculating CSA (issue #388)

2.0.4 (2015-06-06)

• 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

2.0.3 (2015-05-19)

• 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

2.0.2 (2015-05-16)

• 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)

2.0.1 (2015-04-28)

• 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)

2.0 (2015-04-17)

• 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

1.1.2_beta (2014-12-25)

• 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 ).

1.1.1 (2014-11-13)

• FIX: updated ANTs binaries for compatibility with GLIBC_2.13 (issue: https://sourceforge.net/p/spinalcordtoolbox/discussion/help/thread/e00b2aeb/)

1.1 (2014-11-04)

• 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.

1.0.3 (2014-07-30)

• 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

1.0.2 (2014-07-13)

• 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.

1.0.1 (2014-07-03)

• INST: toolbox now requires matplotlib

1.0 (2014-06-15)

• first public release!

0.7 (2014-06-14)

• NEW: dMRI moco

• INST: libraries are now statically compiled

• OPT: propseg: now results are reproducible (i.e. removed pseudo-randomization)

0.6 (2014-06-13)

• 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

0.5 (2014-06-03)

• 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

0.4 (2014-05-28)

• NEW: installer for ANTs (currently only for OSX)

• fixed bugs

0.3 (2014-05-26)

• major changes in sct_register_multimodal

• fixed bugs

0.2 (2014-05-18)

• NEW: nonlocal means denoising filter

• NEW: sct_smooth_spinalcord –> smoothing along centerline

• fixed bugs

0.1 (2014-05-03)

• first beta version!