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Changelog

7.2 (2025-11-28)

View detailed changelog

FEATURE

  • sct_compute_ascor: Add function to compute aSCOR. View pull request
  • sct_deepseg: Add new -test-time-aug flag for nnunetv2 models to turn on use_mirroring behavior. View pull request
  • sct_fmri_moco: Allow specifying a reference scan as the registration target with new flag -ref. View pull request
  • sct_process_segmentation: Update AP diameter to be based on rotated seg + add new -anat flag (for symmetry, quadrant area, and HOG angle properties). View pull request
  • sct_run_batch: Add new -yml arguments to include/exclude both subjects and files based on YAML lists. View pull request

ENHANCEMENT

  • sct_analyze_lesion: Add vert_level column to -f output spreadsheet. View pull request
  • sct_apply_transfo, sct_label_vertebrae, sct_register_multimodal: Improve performance of -x label when applying a warping field to single-voxel point labels. View pull request
  • sct_compute_ascor, sct_process_segmentation: Update -centerline argument to allow for consistent -discfile projection (used in aSCOR script). View pull request
  • sct_deepseg: Rework totalspineseg inference (rename task to spine, set -step1-only behavior as default, improve output filenames). View pull request
  • Hide developer-specific arguments in argparse help. View pull request

BUG

  • sct_compute_ascor, sct_process_segmentation: Update how -discfile intermediate images are saved (output directory, relative paths). View pull request
  • sct_deepseg, sct_qc: Fix cropping and labeling for DeepSeg axial mosaic QC Reports. View pull request
  • sct_process_segmentation: Solve projection anomaly on anisotropic data. View pull request
  • sct_register_multimodal: Fix logging message to correctly print voxel size in centermassrot . View pull request
  • Only create "detailed summary" test files in CI (and only when the directory exists). View pull request

INSTALLATION

  • sct_deepseg: Switch to neuropoly fork of nnunetv2 to support multi-fold "custom trainer" version of lesion_ms. View pull request
  • sct_deepseg: Pin blosc2<3.9.0 to avoid failing PRs due to incompatibility wiht numpy<2.0. View pull request
  • sct_deepseg: Make spinalcord a default model to solve PyTorchStreamReader error in sct_run_batch. View pull request
  • Allow blosc2>=3.9.1 due to re-added support for numpy==1.26. View pull request
  • Restrict numexpr!=2.14.0 and h5py!=3.15.0 to address recent installation failures. View pull request
  • Avoid libffi bug by installing all of the conda packages from conda-forge in a single step. View pull request

DOCUMENTATION

  • sct_deepseg: Added ref for lesion_ms ESMRMB 2025 model. View pull request
  • sct_deepseg: Update spinal rootlets model description. View pull request
  • sct_deepseg: Add citation for RootletSeg model in models.py. View pull request
  • sct_dmri_moco, sct_fmri_moco: Improve moco argparse usage for -param {poly,iter} (help descriptions) and -g (positive integer requirement). View pull request
  • sct_register_to_template: Add tutorial for rootlets-based registration to template. View pull request
  • Replace PaperPile links with PubMed links in pam50.rst doc page. View pull request
  • Update "Citing SCT" page with missing references and better formatting. View pull request
  • Tweak -ref subject-related documentation for 3+ labels. View pull request
  • Update sct_tutorial_data links to point to the newest release (SCT Course 2025). View pull request
  • Fix typos in MS lesion tutorial (ms_lesion -> lesion_ms). View pull request

REFACTORING

  • sct_compute_ascor, sct_process_segmentation: Clarify ValueError if the -centerline does not cover all the slices in the input mask. View pull request
  • sct_deepseg, sct_fmri_compute_tsnr, sct_label_utils, sct_label_vertebrae, sct_qc, sct_register_multimodal, sct_register_to_template: Refactor QC code for six scripts. View pull request

CI

GIT/GITHUB

  • Update pull request template to mention tests requirement (and improve readability). View pull request

7.1 (2025-08-15)

View detailed changelog

FEATURE

  • sct_analyze_lesion: Implement "tissue bridge ratio" metrics. View pull request
  • sct_compute_compression: Allow MSCC to be computed on lesion masks (as an alternative to compression labels). View pull request
  • sct_maths: Implement anisotropic dilation and erosion. View pull request
  • sct_process_segmentation: Add flag -discfile to allow for determining VertLevel using projected disc labels. View pull request

ENHANCEMENT

  • sct_deepseg: Update lesion_ms DeepSeg model from r20241101 to r20250626 (ESMRMB 2025). View pull request
  • sct_deepseg: Add slice numbers to axial mosaic QC reports. View pull request
  • sct_deepseg: Tweak totalspineseg axial mosaic QC report to make it easier to read. View pull request
  • sct_extract_metric: Use centerline of -vertfile for more accurate mapping of vert levels to z slices. View pull request
  • sct_label_vertebrae: Speed up labeling for -discfile by replacing the straightening step with disc projection. View pull request
  • sct_register_multimodal: Mask output of sct_apply_transfo when applying -initwarp during multimodal registration. View pull request
  • sct_run_batch: Improve clarity of terminal errors when a batch script fails. View pull request
  • [EXPERIMENTAL] Add Apptainer installation for use on HPC systems. View pull request
  • Allow the use of custom mapping for sct_label_vertebrae. View pull request
  • Expand LazyLoader usage to improve import times across scripts. View pull request

BUG

  • sct_analyze_lesion: Change interpolated_midsagittal_slice to be saved in the original orientation (instead of RPI). View pull request
  • sct_analyze_lesion, sct_qc: Fix IndexError by more thoroughly applying the SC mask to the lesion image. View pull request
  • sct_deepseg: Fix two small crashes when generating QC reports using -qc-seg. View pull request
  • sct_qc: Update report-ui to v0.1.1. View pull request
  • sct_qc: Use Path.resolve() instead of Path.absolute(). View pull request
  • sct_register_multimodal, sct_register_to_template: Add safeguards to handle when type=imseg is used with rot_method=pca. View pull request
  • sct_register_to_template: Fix check for user's labels against template's labels by adopting issubset. View pull request
  • sct_register_to_template, sct_straighten_spinalcord: Prevent repeated slices during straightening by correctly zeroing out duplicate slices. View pull request
  • Update PAM50 template to r20250730 to fix pixel error in PAM50_rootlets.nii.gz. View pull request

INSTALLATION

  • Update SCT's virtual environment to use Python 3.10 instead of 3.9. View pull request
  • Limit onnx<1.16.2 to fix CI failures on Windows runners. View pull request
  • Add fixes for PyQt5 and onnxruntime to amend our previous switch to Python 3.10. View pull request
  • Validate $SCT_DIR for path-length issues (even for the default directory + non-interactive mode). View pull request
  • Fix failing CI runs for Arch (rl_print_keybindings) and Debian 10 (EOL). View pull request

DOCUMENTATION

  • sct_deepseg: Clean up argparse help to only display arguments and descriptions relevant to specific tasks. View pull request
  • sct_dmri_moco, sct_fmri_moco: Make sure that all useful parameters in ParamMoco are documented in the -h. View pull request
  • Move graymatter model to gray_matter group. View pull request
  • Update and reorganize Docker installation instructions. View pull request

REFACTORING

CI

GIT/GITHUB

  • Simplify SCT's pull request template to match the new Contributing Guidelines. View pull request

7.0 (2025-04-25)

View detailed changelog

FEATURE

  • sct_deepseg: Add the bavaria-quebec nnUNet model for MS lesion and cord segmentation to sct_deepseg model suite. View pull request
  • sct_deepseg: Allow adding -qc-seg to crop the QC generated by sct_deepseg. View pull request
  • sct_deepseg: Add new contrast-agnostic graymatter model. View pull request
  • sct_deepseg: Add -step1-only argument to the totalspineseg task's subparser. View pull request
  • sct_detect_compression: Add new CLI script to predict compression probability. View pull request
  • sct_qc: Add new column to QC report to rank images numerically from 0-9. View pull request
  • sct_register_to_template: Add -lrootlet argument to enable rootlets-informed registration to the PAM50 template. View pull request
  • Add detailed time and memory profiling for CLI scripts. View pull request

ENHANCEMENT

  • sct_compute_compression, sct_download_data: Update PAM50 normalized metrics URL to latest release (r20250321). View pull request
  • sct_analyze_lesion: Update interpolation logic used when determining the midsagittal slice of lesions. View pull request
  • sct_deepseg: Update contrast-agnostic model from v2.5 to v3.0 . View pull request
  • sct_deepseg: Updated sct_deepseg usage to improve clarity and ease of use. View pull request
  • sct_qc: Overhaul the QC report backend to use modern web technologies (Vite/React/Tailwind/Typescript). View pull request
  • sct_resample: Improve clarity of ZeroDivisionError message when resampling. View pull request
  • sct_warp_template: Update PAM50 release links to r20250422 (ventral rootlets, Th1 level). View pull request
  • Change over to MiniForge as the package manager (from MiniConda prior). View pull request
  • Add basic automatic time profiling for all CLI scripts by default. View pull request

BUG

  • sct_deepseg: Preserve the _seg suffix for the contrast-agnostic model. View pull request
  • sct_get_centerline: Update get_centerline to ensure that output arrays match the orientation of the output centerline image. View pull request
  • sct_process_segmentation: Fix slice indexing for -angle-corr-centerline. View pull request
  • sct_qc: Replace pyplot usage in qc.py to address crashing in Jupyter notebooks. View pull request
  • sct_qc: Implement QC outlines for multi-valued segmentations. View pull request

INSTALLATION

  • Change over to MiniForge as the package manager (from MiniConda prior). View pull request
  • Pin torch to <2.3 to keep versions in sync with Intel Mac platforms. View pull request
  • Transfer hotfixes from the test-past-releases.yml CI workflow to the 5.x-6.x series of SCT releases. View pull request
  • Allow ANTs binaries to access msvc-runtime DLLs to avoid DLL not found errors. View pull request
  • Gracefully handle permission issues on RC files during installation. View pull request

DOCUMENTATION

  • sct_apply_transfo: Amend argparse help of transform tool to make -d and -o arguments clearer. View pull request
  • sct_deepseg: Update sct_deepseg documentation and arg help. View pull request
  • sct_deepseg: Fix missed rename of the contrast agnostic model (_monai -> _nnunet). View pull request
  • Update courses.rst with SCT Course 2024 links. View pull request
  • Fix wording in opening paragraph within courses.rst documentation page. View pull request
  • Update web tutorials to match the changes made for the 2024 SCT Course. View pull request
  • Expand "batch processing" tutorial with steps for manual correction. View pull request

REFACTORING

  • sct_deepseg: Use argparse subparsers for sct_deepseg. View pull request
  • sct_deepseg: Retire the model sc_t2star from sct_deepseg (and move its model gallery entry). View pull request
  • Consolidate common elements (-h/-v/-r + argument groups) into SCTArgumentParser. View pull request

CI

6.5 (2024-11-21)

View detailed changelog

FEATURE

  • sct_analyze_lesion: Output lesion length and width for the midsagittal slice. View pull request
  • sct_deepseg: Add -custom-url arg to allow users to install specific .zips for existing deepseg models. View pull request
  • sct_deepseg: Update contrast agnostic model to r20241024 (improved for SCI and whole-spine T1/T2 images). View pull request
  • sct_deepseg: Add contrast-agnostic MS lesion segmentation model. View pull request
  • sct_deepseg: Add canal segmentation model. View pull request and follow-up pull request
  • sct_deepseg: Add TotalSpineSeg model (vertebrae, intervertebral discs, spinal cord, and spinal canal). View pull request
  • sct_deepseg, sct_qc: Add -qc-plane flag to allow switching the QC view to 'Sagittal'. View pull request
  • sct_fmri_compute_tsnr, sct_qc: Add -m (mask) and -qc options to fMRI TSNR script. View pull request
  • sct_get_centerline: Expose space API parameter in centerline CLI to allow user to specify -space phys. View pull request

ENHANCEMENT

  • sct_analyze_lesion: Update extension of lesion analysis spreadsheet from .xls to .xlsx. View pull request
  • sct_analyze_lesion, sct_qc: Swap x-axis in tissue bridges QC. View pull request
  • sct_apply_transfo: Preserve integer dtype when warping an image using NearestNeighbour interpolation. View pull request
  • sct_apply_transfo, sct_warp_template: Use faster dilation algorithm when dilating "mostly zero" point label images (-x label). View pull request
  • sct_dmri_moco, sct_fmri_moco, sct_register_multimodal: Convert softmask to binary mask before passing to ANTs, rather than applying softmask to input data. View pull request
  • sct_download_data: Add an interactive check before deleting output directory when downloading data. View pull request
  • sct_download_data: Update sct_course_data URL to point to SCT-Course-20241209. View pull request

BUG

  • sct_analyze_lesion: Fix crash during lesion analysis if there is no midsagittal lesion. View pull request
  • sct_apply_transfo: Properly maintain verbose status for internal ANTs run_proc call (to silence logging for -v 0). View pull request
  • sct_deepseg: Test EPI model to ensure that it has the correct nnUNetTrainer model structure. View pull request
  • sct_deepseg: Remove faulty zip() that breaks -install option. View pull request
  • sct_deepseg: Fix the suffix of the rootlets model (_seg -> _rootlets) to prevent overwriting. View pull request
  • sct_deepseg: Fix rootlets QC for anisotropic images. View pull request
  • sct_extract_metric: Add more intuitive feedback when no metrics can be extracted from input data. View pull request
  • sct_maths: Fix incorrectly lazy-loaded dipy imports. View pull request
  • sct_maths: Fix dtype mismatch error when mixing integers and floating point numbers. View pull request
  • Add clearer instructions to fix issue when $SCT_DIR isn't writeable during installation. View pull request
  • Fix bug due to discrepancy introduced by set_qform and set_sform methods. View pull request
  • Update warnings filter to properly filter Private repos warning from requirements.parse. View pull request

INSTALLATION

DOCUMENTATION

  • sct_analyze_lesion: Add lesion-analysis tutorial. View pull request
  • sct_deepseg: Add spinal nerve rootlets segmentation tutorial. View pull request
  • sct_deepseg: Add example commands for the -custom-url arg. View pull request
  • sct_deepseg: Retire outdated DeepSeg models (seg_sc_ms_lesion_stir_psir, ms_sc_mp2rage). View pull request
  • Address deprecation by manually performing previous RTD Sphinx context injection . View pull request
  • Split "Command Line Tools" page into multiple individual pages (with markdown formatting for argparse). View pull request
  • Move "Labeling Conventions" page to "Concepts", while preserving tutorial using .. include:: directive. View pull request
  • Remove /en/latest/ slugs from spinalcordtoolbox.com URLs. View pull request
  • Handle newly-broken links (retries, FSLWiki changes). View pull request
  • Apply minor documentation feedback from 2023 SCT course. View pull request
  • Add model gallery for current version of DeepSeg (-task syntax). View pull request
  • Fix hyperlink syntax in documentation (Markdown -> RST). View pull request

CI

  • Skip -h duration test on macOS CI runners due to sporadic runtimes. View pull request
  • Allow error code 406 in broken link checker. View pull request
  • Be good netizens when checking broken links (HEAD request only, 30s retries, respect Retry-All). View pull request
  • Bump oldest macOS version used by test runners (12 -> 13). View pull request

6.4 (2024-08-01)

View detailed changelog

FEATURE

  • sct_analyze_lesion: Automatically compute midsagittal tissue bridges. View pull request
  • sct_analyze_lesion: Support CombinedLabels from info_label.txt when computing lesion distributions with -f. View pull request
  • sct_analyze_lesion: Add -perslice option (plus performance improvements to make it feasible). View pull request
  • sct_compute_flow: New function to compute velocity from VENC sequence. View pull request
  • sct_deepseg: Track sct_deepseg model provenance with source.json (in model folder) and JSON sidecar (in output). View pull request
  • sct_deepseg: Add postprocessing functionality for non-ivadomed models. View pull request
  • sct_download_data: Add T2w dog template to available data downloads. View pull request

ENHANCEMENT

  • sct_deepseg: Change -install-task arg to -install. View pull request
  • sct_deepseg: Update contrast agnostic model to v2.4 (now improved for lumbar t2w + PSIR/STIR images). View pull request
  • sct_deepseg: Indicate model version in "model is up to date" log message. View pull request
  • sct_deepseg: Replace seg_ms_lesion_mp2rage model with a nnUnet based model on sct_deepseg. View pull request
  • sct_deepseg: Fix rootlets QC by improving the cropping, centering, and colormap. View pull request
  • sct_deepseg: Set edge padding as default for contrast-agnostic monai model. View pull request
  • sct_deepseg: Update SCI model to SCIsegV2 and standardize on nnUNetTrainer folder structure. View pull request
  • sct_maths: Allow multiple sct_maths operations to be run sequentially on an image in one command. View pull request
  • sct_maths: Add -volumewise to process the individual 3D volumes of 4D input images. View pull request
  • Run all tests in temporary directories (to preserve a clean copy of sct_testing_data). View pull request

BUG

  • sct_analyze_lesion: Fix crashing if there is no midsagittal lesion. View pull request
  • sct_analyze_lesion: Silence pandas warning by explicitly using copy to remove view/copy ambiguity View pull request
  • sct_analyze_lesion: Fix slice numbering in QC and CLI output View pull request
  • sct_apply_transfo: Make sure that fname_out is set properly for fsleyes command when -o is not passed. View pull request
  • sct_deepseg: Ensure that using -thr 0 with the contrast agnostic model generates a useful softseg. View pull request
  • sct_deepseg: Avoid buggy version of nnunetv2 that produces empty output predictions. View pull request
  • sct_dmri_moco, sct_fmri_moco: Output ANTs syntax in moco functions with -v 2 for easier debugging. View pull request
  • sct_extract_metric: Ignore case where user selects 'combine=1' with CombinedLabels. View pull request
  • sct_extract_metric: Skip empty slicegroups to avoid creating blank rows in output metric CSV file. View pull request
  • sct_flatten_sagittal: Rescale flattened values from [-1.0, 1.0] back to their original range and datatype. View pull request
  • sct_label_vertebrae, sct_register_to_template, sct_smooth_spinalcord: Include the SCT version in the straightening.cache. View pull request
  • sct_qc: Fix tiny sagittal mosaic QC Report for large images with many slices. View pull request
  • sct_qc: Properly detect softsegs for QC when binary values are not the most common values.. View pull request
  • sct_qc: Align the lock names for qc.py and qc2.py. View pull request
  • sct_qc: Adjust QC canvas size by physical resolution to avoid tiny QC with anisotropic T2* images. View pull request
  • sct_qc, sct_run_batch: Increase timeout of mutex to avoid AlreadyLocked errors with many concurrent processes. View pull request
  • sct_register_to_template: Add rotation to landmark-based preregistration (step=0) during template registration. View pull request
  • sct_straighten_spinalcord: Fix straightening transformations for images with "tilted" qform/sform. View pull request
  • Fix small argparse bug when wrapping help text with whitespace-only lines. View pull request
  • Add matplotlib-inline backend for compatibility with Jupyter notebooks. View pull request

INSTALLATION

DOCUMENTATION

  • sct_analyze_lesion: Improve documentation of the -f argument to make the percentages clearer. View pull request
  • sct_analyze_lesion: Improve formatting of bullet points in CLI help. View pull request
  • sct_apply_transfo: Rewrite help for -x label to clarify the difference between single-voxel and multi-voxel labels. View pull request
  • sct_label_utils: Clarify that -disc does not involve orthogonal projection. View pull request
  • sct_run_batch: Clarified how many subjects are processed in parallel. View pull request
  • sct_label_utils: Clarify argument order for -disc. View pull request
  • Update url to slicer documentation. View pull request
  • Update redirected citation link. View pull request

REFACTORING

  • sct_deepseg, sct_deepseg_sc, sct_register_to_template: Remove duplicate functions in sct_deepseg and sct_register_to_template. View pull request
  • sct_maths: Minor improvements to PR #4485. View pull request
  • sct_qc: Refactor qc.py to use create_qc_entry. View pull request
  • Use Tensorflow's simple LazyLoader class to minimize import times of expensive packages. View pull request
  • Simplify calls to np.einsum. View pull request

CI

  • Update github action to Node.js 20. View pull request
  • Replace libglib2.0-0 with t64 version to fix Debian Rolling Release test failure. View pull request
  • Update CentOS Stream 8 runner to work past EOL. View pull request
  • Set norecursedirs in setup.cfg to avoid pytest collecting tests from our dependencies within our venv. View pull request

6.3 (2024-04-25)

View detailed changelog

FEATURE

ENHANCEMENT

  • sct_fmri_moco: Switch to using mean magnitude for output moco_params.tsv file used for QC. View pull request
  • sct_process_segmentation: Add improvements to CSA calculation for GM/WM masks (-angle-corr-centerline, float32 precision fix, doc warnings). View pull request
  • sct_qc: Add padding to the crop used for sagittal mosaic QC report. View pull request
  • sct_qc: Isolate index.html-writing code into reusable script + replace Lock with Semaphore-based mutex. View pull request
  • sct_qc: Switch from two-tone colormap to transparency for sct_deepseg QC. View pull request

BUG

  • sct_deepseg: Address upstream breaking API change by renaming _gpu input param to _device. View pull request
  • sct_deepseg: Avoid nnunetv2=={2.4.0,2.4.1} to mitigate upstream bug for predict_single_npy_array. View pull request
  • sct_qc: Fix -p sct_label_vertebrae QC report when providing TotalSegmentator labels. View pull request
  • sct_qc: Fix detection of PSIR images for QC resampling to avoid unnecessary thresholding. View pull request
  • sct_qc: Keep CSS/JS/etc. assets up to date when QC report is regenerated with a newer version of SCT. View pull request
  • sct_qc: Avoid nibabel crashes due to int64 arrays by explicitly passing dtype/header to Nifti1Image. View pull request
  • sct_run_batch: Filter out color codes from log files. View pull request
  • Update QC assets when saving the QC report. View pull request
  • Replace remaining usages of nib.save() with Image.save() to mitigate scaling issues. View pull request

INSTALLATION

  • Pull upstream ivadomed changes that let us upgrade previously-pinned versions of dipy/numpy/nibabel. View pull request
  • Address test warnings by pinning pyqt5-sip<12.13.0 and updating setup.cfg ignore entries (pkg_resources). View pull request
  • Pin to dipy<1.6 until conflicts with dipy>=1.8 can be resolved. View pull request

DOCUMENTATION

  • sct_extract_metric: Fixed path to PAM50 in help example command. View pull request
  • sct_image: Clarify argparse help for -copy-header option to provide caution about header/data mismatches. View pull request
  • Add links to 2024 review in prominent locations in documentation. View pull request
  • Fix inaccurate line in docs regarding the method used for spinal level estimation (Frostell et al.). View pull request

REFACTORING

  • Restructure QC report code to use create_qc_entry context manager (plus 1 PoC: multimodal). View pull request

CI

  • Update GitHub Actions versions (macOS runners, Windows runners, Node.js 16 actions -> 20). View pull request
  • Update GitHub Actions versions (Debian 9->11, CentOS 7->9, WSL 2022->2019) to fix CI failures. View pull request
  • Add CI workflow step to detect broken links in repository files. View pull request
  • Reduce concurrent macOS runners on PRs from 6 to 2 (and remove push-to-master triggers). View pull request
  • Replace matrix.os with runner.os to more robustly detect Win OSs in GHA workflows. View pull request
  • Move most broken link checking to a daily job. View pull request
  • Fix broken link checker. View pull request

6.2 (2024-02-15)

View detailed changelog

FEATURE

  • sct_deepseg: Integrate NNUnet/MONAI models into DeepSeg CLI (contrast-agnostic, SCI, rootlets, Zurich mouse). View pull request
  • sct_qc: Save QC records to browser local storage. View pull request
  • sct_warp_template: Update PAM50 link to include new template/PAM50_rootlets.nii.gz file. View pull request

ENHANCEMENT

  • Convert integer images to floating point when resampling with linear interpolation. View pull request

BUG

  • sct_analyze_lesion: Set minmax=False to prevent cropping during angle correction, avoiding slice number mismatches. View pull request
  • sct_compute_compression: Fix reversed slice numbering (S->I => I->S) in output CSV file. View pull request
  • sct_compute_mtsat: Apply missing B1 correction to r1map and a calculations to fix MTsat bug. View pull request
  • sct_deepseg: Reverse spacings to match nnUNet's SimpleITK-based conventions. View pull request
  • sct_deepseg, sct_label_vertebrae: Mitigate scaling issues (1.0 -> 0.999) due to float/int datatype mismatches between header and array. View pull request
  • sct_label_vertebrae: Fix path splitting when space (' ') is present in isct_spine_detect model path. View pull request
  • sct_register_to_template: Ensure reorientation is performed consistently before any resampling. View pull request
  • sct_register_to_template: Fix straightening error during registration if 3+ labels are supplied and topmost disc label is not C1. View pull request

INSTALLATION

  • Temporary fix for dependency issue with dipy 1.8.0. View pull request
  • Fix broken pip installer by forcing it to detect macOS 11 as 11.0 and not 10.16. View pull request
  • Document Rosetta 2 as a requirement for installation on Apple silicon (M1, M2, M3). View pull request

DOCUMENTATION

  • sct_compute_compression: Update argparse descriptions to make it clear that the script can also be used to compute MCC. View pull request
  • sct_label_utils: Clarify the argparse help description for the -disc argument. View pull request
  • sct_run_batch: Add example syntax for YAML and JSON config files to the argparse help description for exclude_list. View pull request
  • sct_run_batch: Add examples to -include-list and -exclude-list flags. View pull request
  • Add links to both the slide deck and YouTube video for the 2023 SCT Course. View pull request
  • Port changes from SCT Course 2023 Google Slides to the web tutorials. View pull request
  • Update sphinx and furo while removing "Edit on GitHub" hack in the process. View pull request

REFACTORING

CI

6.1 (2023-11-03)

View detailed changelog

FEATURE

  • sct_analyze_lesion: Add function to output the axial damage ratio + minor improvements. View pull request
  • sct_download_data: Add current sct_tutorial_data release as a new course dataset. View pull request
  • sct_download_data: Update PAM50 template link to include cord and lumbar label changes. View pull request
  • sct_run_batch: Add start date information to the logs. View pull request

ENHANCEMENT

  • sct_compute_compression: Improvements of CLI output printed by the sct_compute_compression. View pull request
  • sct_deepseg: Append -list-tasks to argparse help and update -list-tasks-long. View pull request
  • sct_label_utils: Speed up -remove-reference by removing unnecessary iteration. View pull request
  • sct_run_batch: Raise error if -config file has wrong suffix. View pull request

BUG

  • sct_compute_compression: Use pandas for .csv saving to correctly merge existing output metric columns. View pull request
  • sct_deepseg: Add checks for empty arrays post-segmentation. View pull request
  • sct_deepseg: Update model releases (lumbar_seg, t2star_sc) to fix output suffix (_seg-manual -> _seg). View pull request
  • sct_dmri_compute_dti: Avoid dipy versions 1.6.0 + 1.7.0 that contain a method=restore bug. View pull request
  • sct_dmri_display_bvecs: Fix ValueError by passing a tuple to color= instead of a numpy array. View pull request
  • sct_label_vertebrae: Check whether the provided discfile is empty. View pull request
  • sct_propseg: Remove parent parts from fname_out to fix buggy -o behavior. View pull request
  • sct_qc: Fix QC for soft segmentations that have light regions close to 1.0 (e.g. 0.999). View pull request
  • sct_register_to_template: Raise exception if sform/qform don't match during registation. View pull request
  • sct_register_to_template: Avoid duplicate orthogonal labels during registration by checking existing labels first. View pull request
  • sct_register_to_template: Switch matmul syntax (* -> @) to follow-up previous np.matrix -> np.array change. View pull request
  • sct_straighten_spinalcord: Fix IndexError during straightening if -dest image is shorter than centerline image (-s). View pull request
  • Gracefully handle infinity as well as NaN values in QC. View pull request
  • Fix distorted registration due to straightening bug in get_closest_to_absolute. View pull request
  • Temporarily pin onnxruntime to <1.16. View pull request
  • Avoid onnxruntime 1.16.0 but allow onnxruntime >=1.16.1. View pull request

INSTALLATION

DOCUMENTATION

  • sct_compute_compression: Add tutorial for sct_compute_compression in documentation. View pull request
  • sct_compute_compression, sct_process_segmentation: Add references for PAM50 normalized metrics. View pull request
  • sct_download_data: List sct_download_data datasets at the end of -h. View pull request
  • sct_download_data: Color installed datasets for sct_download_data -h. View pull request
  • sct_run_batch: Clarification of sct_run_batch -script-args input flag help. View pull request
  • sct_run_batch: Add note that ~ should not be used in paths passed using the -script-args arg. View pull request
  • Update installation docs for Windows (Miniconda) and Linux/macOS (standalone installer). View pull request
  • Migrate old ReadTheDocs settings to .readthedocs.yaml. View pull request
  • Update documentation for new spinal levels. View pull request
  • Disable PDF and EPUB documentation builds. View pull request
  • Update figure and references for "Other shape metrics" tutorial. View pull request
  • Fix typo in "Other shape metrics" tutorial. View pull request
  • Add tutorial for lumbar segmentation and registration. View pull request

REFACTORING

  • sct_analyze_lesion: Simplify lesion volume computation. View pull request
  • sct_compute_compression: Use the pandas.DataFrame.combine_first method. View pull request
  • sct_warp_template: Remove -s functionality and add a deprecation warning. View pull request

CI

  • Exit on errors anywhere in the linter script. View pull request
  • Update changelog PR workflow to fix milestone title error and to also change version.txt. View pull request

6.0 (2023-07-14)

View detailed changelog

FEATURE

  • sct_analyze_lesion: Allow lesion volume calculation without providing SC seg. View pull request
  • sct_compute_compression: Add new CLI script to compute normalized metric ratios (MSCC, etc.) for compressed levels. View pull request
  • sct_crop_image: Add -dilate option to enable cropping around a spinal cord segmentation. View pull request
  • sct_deepseg: Add support for model ensembles to sct_deepseg, update mp2rage_lesion model. View pull request
  • sct_deepseg_lesion, sct_qc: Add sagittal mosaic QC and use it for sct_deepseg_lesion QC report. View pull request
  • sct_get_centerline: Add -centerline-soft option to output a non-binary "soft" centerline. View pull request
  • sct_image: Replace -setorient-data with -flip and -transpose options. WARNING: Breaks compatibility with previous version. View pull request
  • sct_label_utils: Add new project_centerline option in sct_label_utils to project an image on the spinal cord centerline . View pull request
  • sct_process_segmentation: Bring metrics in PAM50 anatomical dimensions in sct_process_segmentation. View pull request
  • sct_process_segmentation: Display vertebral levels when provided with -perslice 1. View pull request
  • sct_warp_template: Add new -histo option to warp the newly-added PAM50 histology files. View pull request
  • sct_register_to_template: List resampled labels in order. View pull request

ENHANCEMENT

  • sct_detect_pmj: Add -qc-dataset and -qc-subject flags to sct_detect_pmj.py. View pull request
  • sct_image: Add -qc-subject and -qc-dataset flags to sct_image. View pull request
  • sct_label_utils: Update labelize_from_discs() to add level labels above the top disc and below the bottom disc. View pull request
  • sct_maths: Use filters.rank instead of dilate/erode for uint8/uint16 images. View pull request
  • sct_propseg: Silence unnecessary "overwriting" messages when updating output image header. View pull request
  • Fix indentation for wrapped lines in argparse help. View pull request
  • Fix broken tqdm behavior for Windows and older Unix platforms. View pull request
  • Use sct_progress_bar for algo=columnwise and register2d slicewise loops. View pull request
  • Replace algo=rigid with algo=slicereg for mt0-mt1 registration. View pull request
  • Selectively display relpath or abspath in viewer syntax based on CWD. View pull request

BUG

  • sct_analyze_texture: Change grey --> gray in imports of skimage.feature functions. View pull request
  • sct_compute_ernst_angle: Fix upper/lower TR bounds used when plotting Ernst angles (argument -b). View pull request
  • sct_deepseg: Clean up improper submodule access (via imported parent modules). View pull request
  • sct_deepseg_lesion: Fix broken -v 2 case by making sure fname_res_ctr exists prior to resampling. View pull request
  • sct_deepseg_sc: Ensure that qform/sform codes are preserved when generating segmentation. View pull request
  • sct_get_centerline: Prevent soft centerline being used with non fitseg methods. View pull request
  • sct_get_centerline: Add extrapolation for sct_get_centerline fitseg. View pull request
  • sct_image: Swap order of sct_image -stitch QC images to fix incorrect YML path. View pull request
  • sct_label_utils: Fix buggy -create-viewer behavior on initialization (undo crash, blank checkboxes). View pull request
  • sct_plugin.py (FSLeyes): Catch errors from outdated wxpython versions bundled with FSL, then suggest a solution. View pull request
  • sct_qc: Faithfully display sct_qc arguments, rather than making a fake command. View pull request
  • sct_qc: Ensure that sagittal images (and softsegs) are resampled correctly for lesion QC. View pull request
  • sct_qc: Fix errors in the list of available QC processes (index.html, sct_qc.py). View pull request
  • sct_register_to_template: Ensure that the straightening.cache file is output to the PWD during template registration. View pull request
  • sct_resample: Update -mm and -ref argument descriptions, fix parse.error logic, and add tests. View pull request
  • Pin numpy<1.24 to mitigate incompatibility with pystrum==0.2. View pull request
  • Better isolate the SCT conda env by using -p instead of -n during creation. View pull request
  • Make matplotlib less verbose. View pull request
  • Use importlib.metadata to fetch list of scripts instead of pkg_resources. View pull request

INSTALLATION

DOCUMENTATION

  • sct_deepseg: Move MP2RAGE cropping comment from "model" description to "task" description. View pull request
  • sct_deepseg_lesion: Update description of -file_centerline flag to mention -centerline file instead of -centerline manual. View pull request
  • sct_register_multimodal: Add an example -param configuration to the argparse help description of algo=dl. View pull request
  • Improve the readability of temporary directory names throughout SCT. View pull request
  • Add link to mailing list. View pull request
  • Improve the appearance of spinalcordtoolbox.com in search results. View pull request
  • Standardize Python file headers for copyright and license information. View pull request
  • Encode emoji in utf-8. View pull request
  • Clarify documentation for compute_vertebral_distribution. View pull request

REFACTORING

CI

GIT/GITHUB

5.8 (2022-12-02)

View detailed changelog

FEATURE

  • sct_image: Add new -stitch option that wraps stitching functionality from Glocker et al.. View pull request
  • sct_process_segmentation: Add DistancePMJ when perslice flag in sct_process_segmentation. View pull request
  • sct_run_batch: Add -ignore-ses flag to process sub- directories even when ses- subdirectories are present. View pull request

ENHANCEMENT

  • Update header dtype property on save/load to match the datatype of the data array. View pull request
  • sct_analyze_lesion, sct_analyze_texture, sct_denoising_onlm: Enforce use of display_viewer_syntax in four scripts using hardcoded fsleyes commands. View pull request
  • sct_get_centerline: Ensure that the output of get_centerline() can be saved using -r 0. View pull request
  • sct_image: Update binaries_linux to include a rebuilt version of stitching that targets centos7. View pull request
  • sct_label_vertebrae, sct_qc: Add readability fixes for QC reports (sagittal view scaling, label text, label colormaps). View pull request
  • sct_register_multimodal: Add dimensions of data to registration logging. View pull request
  • sct_register_multimodal: Minimize memory usage for algo=dl (and add a warning for potential OOM killer issues). View pull request
  • sct_register_to_template: Throw error when labels are lost during the straightening transform. View pull request

BUG

  • Properly escape \ in the regex for removing sct_env from old RC files. View pull request
  • Ensure that calling printv(type='error') actually exits the program. View pull request
  • Reduce logging from intermediate CLI scripts by setting -v 0 in main() calls. View pull request
  • Address [Errno 24] Too many open files during motion correction. View pull request
  • Fix several bugs when loading headers in the Image constructor. View pull request
  • Set a more permissive quaternion_threshold inside Image constructor. View pull request
  • sct_analyze_lesion: Fix output filename spelling. View pull request
  • sct_check_dependencies: Re-add print_line call for PropSeg check. View pull request
  • sct_extract_metric: Ensure that -list-labels is the last argument that is parsed. View pull request
  • sct_get_centerline: Exclude original file extension (e.g. .nii.gz) from the output .csv filename. View pull request
  • sct_merge_images, sct_smooth_spinalcord: Enforce type=int for arguments that use choices=(0, 1). View pull request
  • sct_propseg, sct_straighten_spinalcord: Pass argv to generate_qc functions (instead of arguments or sys.argv[1:]). View pull request
  • sct_register_multimodal: Improve handling of case where algo is specified alongside type='label'. View pull request
  • sct_run_batch: Modify -include-list and -exclude-list to check against parts of a directory, too. View pull request
  • sct_run_batch: Fix include_list/exclude argument ordering in call to _filter_directories. View pull request
  • sct_run_batch: Allow path_output parameter to start with ~. View pull request
  • install_sct.bat: Use delayed expansion (!!) for git_ref. View pull request

INSTALLATION

  • Upgrade SCT from Python 3.7 to Python 3.8. View pull request
  • Limit pyqt5 to >5.11 and <5.15 to avoid "Cannot load library libqxcb.so" error on Ubuntu. View pull request
  • Ensure bundled GLIBC is up-to-date in order to resolve MESA-LOADER errors. View pull request
  • Add more thorough check for git within the PATH for the Windows installer. View pull request

DOCUMENTATION

REFACTORING

  • Replace run_proc calls with main calls across SCT's scripts. View pull request
  • Replace argv=None default by argv: Sequence[str] type hint. View pull request
  • Simplify add_suffix. View pull request
  • Move 5 unused scripts to spinalcordtoolbox-dev. View pull request
  • Remove unused isct_ scripts from SCT's CLI and test suite. View pull request
  • sct_check_dependencies: Convert isct_test_ants script into a pytest test, then call via sct_check_dependencies. View pull request
  • sct_compute_snr, sct_dmri_moco, sct_fmri_moco, sct_maths, sct_process_segmentation: Call parser.error properly. View pull request
  • sct_dmri_denoise_patch2self: Deal with nibabel deprecation of get_header and get_data. View pull request
  • sct_download_data: Refactor data downloading API to remove dependency on CLI script. View pull request
  • sct_merge_images: Tidy up PEP8 warnings and other small style issues. View pull request
  • sct_process_segmentation: Improve handling of default arguments. View pull request
  • math.py: Address selem deprecation by using footprint. View pull request
  • shell.py: Let Metavar inherit from str to silence PyCharm type warning. View pull request

CI

5.7 (2022-07-28)

View detailed changelog

FEATURE

  • sct_process_segmentation,sct_extract_metric: Combine conditions when slice number and vertebral levels are both specified. View pull request
  • sct_register_to_template,sct_register_multimodal: Integration of DL multimodal registration in SCT. View pull request
  • Allow in-place installations (to support PRs from forks). View pull request

CI

BUG

  • sct_propseg: Prevent from overwriting files by outputting to a tempdir prior to renaming. View pull request
  • sct_maths: Swap if for elif to prevent error from being thrown when calling sct_maths -mi. View pull request
  • sct_merge_images: Remove catch-all exception handling. View pull request
  • image.py: Use shutil.copyfile for output files if src/dest are on different filesystems. View pull request
  • sct_process_segmentation: Move CSA normalization models to ./data/ at the root of the SCT repo. View pull request
  • sct_maths: Rewrite -add/-sub/-mul/-div to match expected behavior for 3D/4D images. View pull request
  • image.py: Use absolutepath when loading images. View pull request

INSTALLATION

  • Repair automated commenting out of pre-4.0 sct settings. View pull request
  • requirements.txt: Pin protobuf to fix upstream Keras issue. View pull request
  • Replace pushd/popd with cd-in-a-subshell. View pull request
  • requirements.txt: Use CPU --extra-index-url to remove strict dependency pinning for torch. View pull request
  • sct_download_data: Use binaries that are packaged by the spinalcordtoolbox-binaries repo. View pull request

DOCUMENTATION

ENHANCEMENT

  • sct_check_dependencies: Clean up FSLeyes version checking to be less verbose/confusing. View pull request
  • fslhd: Account for None orientation strings when printing image headers. View pull request
  • sct_deepseg_sc,sct_deepseg_gm,sct_deepseg_lesion: Replace Tensorflow/Keras-based inference (.h5) with onnxruntime (.ONNX). View pull request

REFACTORING

  • utils.py: Unify calls to shutil.move by using only utils.fs.mv. View pull request
  • Reduce flake8 warnings throughout the codebase. View pull request
  • sct_label_vertebrae: Remove deprecation warning for previously-removed gaussian_std argument. View pull request
  • Fix executable file permissions and remove unnecessary header declarations. View pull request
  • aggregate_slicewise.py: Update docstring for the aggregate_per_slice_or_level function. View pull request
  • sct_register_to_template,sct_register_multimodal: Fix circular and star importing in registration CLI scripts. View pull request

GIT/GITHUB

5.6 (2022-04-29)

View detailed changelog

FEATURE

CI

BUG

  • sct_deepseg: Rewrite ANSI color code snippets to support terminals limited to 16-colors. View pull request
  • sct_label_vertebrae: Output a better error message when the initial disc is invalid. View pull request
  • Set a more permissive threshold for reading the qform. View pull request
  • sct_check_dependencies: Skip checking isct_propseg on Windows. View pull request
  • sct_analyze_texture: Stop using a tempfile for data reorientation. View pull request
  • Open CSV files using newline='' to fix \r\r\n issue. View pull request
  • sct_run_batch: Check isdir directly, rather than trying to catch IsADirectoryError. View pull request
  • sct_dice_coefficient: Update CMakeLists.txt to include bugfix for unresolved external symbol errors. View pull request
  • sct_run_batch: Account for non-UNIX platforms in sys.platform checks. View pull request
  • Replace hardcoded /tmp directory with tmp_path. View pull request
  • Clean-up Windows-incompatible hardcoded / path separators. View pull request
  • sct_run_batch: Add better support for shell script batch processing on Windows. View pull request
  • Improve how image overwriting is handled for memory-mapped data arrays on Windows. View pull request
  • sct_propseg: Attempt to fixup isct_propseg build (but ultimately skip sct_propseg on Windows). View pull request
  • sct_label_vertebrae: Refactor -param parsing to address several bugs. View pull request
  • sct_propseg: Fix parsing of -d argument in script. View pull request
  • sct_analyze_lesion: Fix computation of estimated lesion length and diameter. View pull request
  • Rewrite QC test to use Pool.close() to avoid stalling with pytest-cov. View pull request
  • sct_get_centerline: Stop appending .nii.gz to the centerline output filepath if -o has an extension. View pull request

INSTALLATION

DOCUMENTATION

ENHANCEMENT

REFACTORING

5.5 (2022-01-26)

View detailed changelog

FEATURE

  • sct_deepseg: Add models for MP2RAGE SC and MS lesion segmentation. View pull request
  • sct_testing: Bring back previously-removed command as a light wrapper for pytest. View pull request
  • sct_deepseg: Add spinal cord/gray matter multiclass segmentation model for 7T data. View pull request
  • sct_dmri_denoise_patch2self: Add new Patch2Self CLI script for dMRI denoising. View pull request

CI

BUG

INSTALLATION

DOCUMENTATION

ENHANCEMENT

  • sct_download_data: Add default output folders for dataset downloads. View pull request

REFACTORING

  • Remove channel=None bugfix that was superseded by upstream skimage=0.19.1 patch. View pull request

GIT/GITHUB

5.4 (2021-09-24)

View detailed changelog

FEATURE

  • sct_process_segmentation: Add CSA normalization in sct_process_segmentation. View pull request
  • sct_register_multimodal: Add -owarpinv to sct_register_multimodal. View pull request
  • sct_maths: Introduce -uthr (upper threshold) to complement -thr (lower threshold) in sct_maths. View pull request
  • sct_process_segmentation: Add PMJ-based CSA in batch_processing.sh. View pull request
  • sct_compute_snr: Implement new method to compute SNR on a single 3D volume. View pull request
  • sct_process_segmentation: Measure CSA based on distance from pontomedullary junction (PMJ). View pull request
  • sct_process_segmentation,sct_qc: Add QC report for sct_process_segmentation for PMJ-based CSA. View pull request
  • sct_compute_snr: Add -o argument to output SNR value to a text file. View pull request
  • sct_qc: Display soft segmentation in qc report. View pull request
  • sct_run_batch: Make it possible to loop across "ses-" entity. View pull request
  • sct_dmri_display_bvecs: Allow sct_dmri_display_bvecs.py to display multi-shell acquisition. View pull request

CI

BUG

  • sct_check_dependencies: Import pyplot before PyQt to mitigate a finicky libgcc_s.so.1 error. View pull request
  • sct_smooth_spinalcord: Fix the output files of sct_smooth_spinalcord (smooth.nii.gz, straight_ref.nii.gz). View pull request
  • Fix-up broken test for sct_compute_snr. View pull request
  • sct_register_to_template,sct_register_multimodal: Apply softmask workaround to slicereg algorithm. View pull request
  • sct_qc: Fix display of PMJ in QC report. View pull request
  • sct_qc: Check if input segmentation is binary for QC report. View pull request
  • sct_plugin.py (FSLeyes): Fix FSLeyes script to make it compatible with both FSLeyes v0.34 and v1.0. View pull request
  • Don't set the global loglevel when CLI scripts are called in-code. View pull request
  • sct_register_multimodal: Don't output dest->src files if registration is only performed one-way. View pull request
  • sct_propseg: Fix rescale_header is not 1 because the default value is 1.0. View pull request
  • sct_process_segmentation: Prevent metric calculation for empty slices by checking if array is ~0. View pull request
  • sct_label_utils: Ensure a copy of the header is used in zeros_like to fix -create-viewer bug. View pull request
  • sct_dmri_display_bvecs: Add test for sct_dmri_display_bvecs, then add -v argument to make the test pass. View pull request
  • sct_dmri_moco: Fix -bvals filepath handling and update bvals argparse help. View pull request
  • sct_resample: Make sure TR parameter isn't lost when resampling 4D images. View pull request
  • sct_apply_transfo: Change sct_apply_transfo -v 0 to match isct_antsApplyTransform output. View pull request

INSTALLATION

  • sct_check_dependencies: Don't crash on non-ImportError exceptions when checking dependencies. View pull request
  • Stop trying to detect headless systems using DISPLAY, and no longer set MPLBACKEND. View pull request
  • Throw error during installation if $SCT_DIR contains spaces. View pull request

DOCUMENTATION

ENHANCEMENT

REFACTORING

GIT/GITHUB

  • Replace neuropoly/spinalcordtoolbox with spinalcordtoolbox/spinalcordtoolbox. View pull request

5.3.0 (2021-04-25)

View detailed changelog

FEATURE

  • sct_image: Handle affine matrix mismatches better by exposing -set-qform-to-sform. View pull request
  • sct_extract_metric: Implemented weighted median. View pull request
  • sct_dmri_moco,sct_fmri_moco,sct_qc: Implement QC for sct_dmri_moco and sct_fmri_moco. View pull request
  • sct_image: Add flag to sct_image to print image headers. View pull request
  • sct_download_data: Add entry to download exvivo template. View pull request
  • sct_register_to_template: Added flag -s-template-id to use another segmentation (e.g. white matter) for registration to template. View pull request
  • sct_qc: Interactive QC assessment: Add Pass/Fail/Artifact and download YAML file. View pull request

CI

BUG

  • sct_run_batch: Fully isolate the conda env by its site.py. View pull request
  • sct_image: Various fixes to sct_image -display-warp. View pull request
  • sct_image: Fix faulty check for arguments.set_sform_to_qform. View pull request
  • sct_deepseg: Update model and fixed default output suffix. View pull request
  • Update outdated sct_register_graymatter command in batch_processing.sh. View pull request
  • sct_run_batch: Unset PYTHONNOUSERSITE in environment before calling batch script. View pull request
  • sct_register_to_template: Fixed right-left flip if template is not RPI and other minor improvements. View pull request
  • Use less strict value for rel_tolerance in the batch_processing.sh test. View pull request
  • sct_deepseg: Unpin ivadomed to get latest version and fix wrong q/sform_code output. View pull request
  • Replace instances of 'sct_convert.convert' with 'image.convert'. View pull request
  • sct_label_vertebrae,sct_warp_template: Replace ANTs binary call with sct_apply_transfo call to properly set sform. View pull request
  • sct_create_mask: Create 2d masks in memory instead of via intermediate files. View pull request
  • sct_label_vertebrae: Handle 'label_discs' case where SC segmentation has holes/discontinuities. View pull request
  • sct_dice_coefficient: Uniquely distinguish filenames for tmp files to prevent overwriting. View pull request
  • Decrease the sensitivity of the sform/qform mismatch check. View pull request

DOCUMENTATION

ENHANCEMENT

GIT/GITHUB

5.2.0 (2021-02-24)

View detailed changelog

FEATURE

  • sct_deepseg: New segmentation model: GM and WM for exvivo DWI data (University of Queensland). View pull request

BUG

DOCUMENTATION

ENHANCEMENT

REFACTORING

  • sct_image: Refactor sct_image functions to accept Image objects as input . View pull request
  • sct_maths: Refactor sct_maths callers to remove subprocess and use API. View pull request

GIT/GITHUB

5.1.0 (2021-01-22)

View detailed changelog

FEATURE

DOCUMENTATION-INTERNAL

BUG

  • sct_compute_hausdorff_distance,sct_dmri_compute_dti: Fix bugs introduced by recent init step refactoring pull request. View pull request
  • sct_propseg: Replace os.path.dirname with pathlib.Path().parent. View pull request
  • sct_deepseg,sct_run_batch: Make sure (most) scripts return error code and print usage when no args are passed. View pull request
  • sct_label_utils: Add new '-create-seg-mid' option to replace bugged '-create-seg -1' behavior. View pull request
  • Replace "argv if argv else '--help'" behavior with subclassed ArgumentParser. View pull request
  • Replace troublesome unicode quote characters with more friendly ones. View pull request
  • Fixup realpath polyfill. View pull request
  • Fix incorrect indexing in get_center_spit to prevent QC report cropping. View pull request
  • Forces output label image to be UINT8 with -create-viewer. View pull request
  • Check that conda actually activated during install.. View pull request
  • sct_label_vertebrae: Change Error type so program doesn't quit when labels are too high. View pull request
  • Set PYTHONNOUSERSITE=True to prevent user site packages from interfering. View pull request
  • Bump ivadomed version to 2.5.0. View pull request
  • sct_label_vertebrae: Fixed missing top disc label with using -discfile . View pull request
  • sct_label_vertebrae: Obsolete -denoise functionality. View pull request
  • Fix API importing scripts. View pull request

INSTALLATION

DOCUMENTATION

ENHANCEMENT

  • Various improvements for the manual labeling of cord centerline. View pull request
  • sct_deepseg: Add option to have a custom task. View pull request
  • sct_run_batch: Print actual numbers of jobs run in parallel.. View pull request
  • Update tumor segmentation models. View pull request
  • Change default option values to None. View pull request
  • sct_deepseg_sc,sct_detect_pmj,sct_propseg: Implement -o flag for a few functions. View pull request
  • sct_label_utils: Update -create-viewer argument to use parse_num_list function. View pull request
  • sct_label_vertebrae: Check that there is two inputs for initz. View pull request
  • sct_register_multimodal: Introduced flags samplingStrategy and samplingPercentage for ANTs calls; Set default to 'None' to ensure reproducible results. View pull request

REFACTORING

GIT/GITHUB

5.0.1 (2020-11-12)

View detailed changelog

CI

BUG

  • sct_process_segmentation: Add missing type information to argument in sct_process_segmentation. View pull request
  • Pin onnxruntime==1.4.0 to avoid libomp issue on macOS. View pull request

DOCUMENTATION

ENHANCEMENT

  • sct_run_batch: sct_run_batch: handle the case of unexecutable script. View pull request
  • sct_label_utils: sct_label_utils.py: Add message for generated files. View pull request
  • Display command when scripts are called from the command-line. View pull request

REFACTORING

  • sct_deepseg: Refactor deepseg/core.py into sct_deepseg and update relevant test. View pull request

5.0.0 (2020-11-07)

View detailed changelog

FEATURE

BUG

INSTALLATION

DOCUMENTATION

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

ENHANCEMENT

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

INSTALLATION

TESTING

4.2.2 (2020-02-28)

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BUG

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

4.2.1 (2020-01-14)

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BUG

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

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

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

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)

View detailed changelog

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

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

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

INSTALLATION

4.0.0 (2019-08-04)

View detailed changelog

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

TESTING

v3.2.7 (2018-10-29)

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BUG

ENHANCEMENT

v3.2.6 (2018-10-16)

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BUG

ENHANCEMENT

FEATURE

v3.2.4 (2018-08-24)

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BUG

ENHANCEMENT

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

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

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

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

ENHANCEMENT

DOCUMENTATION

INSTALLATION

TESTING

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

ENHANCEMENT

FEATURE

3.1.1 (2018-02-16)

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BUG

ENHANCEMENT

FEATURE

TESTING

v3.1.0 (2017-10-27)

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BUG

ENHANCEMENT

FEATURE

TESTING

v3.0.8 (2017-09-13)

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BUG

ENHANCEMENT

FEATURE

v3.0.7 (2017-08-02)

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BUG

ENHANCEMENT

FEATURE

TESTING

DOCUMENTATION

v3.0.6 (2017-07-04)

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BUG

ENHANCEMENT

DOCUMENTATION

INSTALLATION

v3.0.5 (2017-06-09)

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BUG

ENHANCEMENT

FEATURE

v3.0.4 (2017-05-19)

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BUG

ENHANCEMENT

FEATURE

TESTING

v3.0.3 (2017-04-26)

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BUG

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

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

FEATURE

TESTING

v3.0.1 (2017-03-22)

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FEATURE

v3.0.0 (2017-03-15)

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BUG

ENHANCEMENT

TESTING

3.0_beta32 (2017-02-10)

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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

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)

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!