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Merge pull request #2 from Medical-Image-Analysis-Laboratory/dev-pgd-hk
Served for the developement of the second version of MIALSRTK with developement of a workflow library in Python and the distribution of a BIDS App. It includes in particular the following commits (auto-generated with: ``git log v1.0..HEAD --pretty=format:' * %s %Cgreen(%cr) - commit %Cred%h%Creset - %Cblue(%an)' --abbrev-commit``): * DOC: disable custom fvset and makeindex as they do not work properly [skip ci] (2 hours ago) - commit 31ef25a - (Sébastien Tourbier) * DOC: reuse fvset to adjust code but seems to still not working [skip ci] (2 hours ago) - commit f2d2333 - (Sébastien Tourbier) * DOC: an other try to fix column of index for pdf in conf.py [skip ci] (2 hours ago) - commit 8727491 - (Sébastien Tourbier) * DOC: install dejavu font for PDF in conf.py [skip ci] (3 hours ago) - commit 3e3ef25 - (Sébastien Tourbier) * DOC: try to fix customization of font family for latex in conf.py [skip ci] (3 hours ago) - commit 6d5cc09 - (Sébastien Tourbier) * DOC: install fontspec for latex in conf.py [skip ci] (3 hours ago) - commit c0577a4 - (Sébastien Tourbier) * DOC: install fontspec for latex in conf.py [skip ci] (3 hours ago) - commit d6ab04f - (Sébastien Tourbier) * DOC: fix latex_elements in conf.py [skip ci] (3 hours ago) - commit ef1c7e1 - (Sébastien Tourbier) * DOC: adjust code size and improve comments for latex in conf.py [skip ci] (3 hours ago) - commit 588ca2f - (Sébastien Tourbier) * DOC: update customization latex and removed to show version in conf.py [skip ci] (4 hours ago) - commit 798b6d4 - (Sébastien Tourbier) * DOC: comment latex_engine definition in conf.py [skip ci] (4 hours ago) - commit 5e22e1b - (Sébastien Tourbier) * DOC: update readthedocs conf.py for better PDF generation [skip ci] (4 hours ago) - commit 874d856 - (Sébastien Tourbier) * DOC: reviewed more text highlights [skip ci] (16 hours ago) - commit d0b7de2 - (Sebastien Tourbier) * DOC: reviewed about in README and index.rst and modified text highlight [skip ci] (17 hours ago) - commit dedb53e - (Sebastien Tourbier) * DOC: fix typo in contributing.rst [skip ci] (17 hours ago) - commit 72d80ba - (Sebastien Tourbier) * DOC: move one level up section "not list as contributor?" in contributing.rst [skip ci] (17 hours ago) - commit e73bcab - (Sebastien Tourbier) * DOC: renamed title to Pipelines module in api_pipelines.rst [skip ci] (17 hours ago) - commit 32e934f - (Sebastien Tourbier) * DOC: Add missing contribution type section title in contributing.rst [skip ci] (17 hours ago) - commit 86085eb - (Sebastien Tourbier) * DOC: shorten title to Contributing in contributing.rst [skip ci] (17 hours ago) - commit 1a8b6b2 - (Sebastien Tourbier) * DOC: update info to add contributor to the list [skip ci] (18 hours ago) - commit a0b7514 - (Sebastien Tourbier) * DOC: update info to add contributor to the list [skip ci] (18 hours ago) - commit 32e46bd - (Sebastien Tourbier) * DOC: update info to add contributor to the list [skip ci] (18 hours ago) - commit aafe470 - (Sebastien Tourbier) * DEL: Remove empty scripts/superresolution script and folder [skip ci] (19 hours ago) - commit 99372f7 - (Sebastien Tourbier) * DOC: add info to add contributor to the list in the README [skip ci] (19 hours ago) - commit 1e55459 - (Sebastien Tourbier) * DOC: reviewed level of markers for section/subsection title in index.rst [skip ci] (22 hours ago) - commit 66465dc - (Sebastien Tourbier) * DOC: reviewed latex settings for PDF generation in conf.py [skip ci] (22 hours ago) - commit 25a4352 - (Sebastien Tourbier) * DOC: reviewed level of markers for section/subsection title in index.rst [skip ci] (23 hours ago) - commit 87eef77 - (Sebastien Tourbier) * DOC: make the line below headers bigger in table of outputs.rst [skip ci] (23 hours ago) - commit 367fe54 - (Sebastien Tourbier) * DOC: resized images in outputs.rst [skip ci] (23 hours ago) - commit 72e50d0 - (Sebastien Tourbier) * DOC: resized logo in index.rst [skip ci] (23 hours ago) - commit e774e3e - (Sebastien Tourbier) * DOC: resized logo in index.rst [skip ci] (23 hours ago) - commit 4304257 - (Sebastien Tourbier) * DOC: reviewed labels for generalization in outputs.rst [skip ci] (23 hours ago) - commit ac55522 - (Sebastien Tourbier) * DOC: fix bids entities table in outputs.rst [skip ci] (24 hours ago) - commit 95d0191 - (Sebastien Tourbier) * DOC: fix bids entities table in outputs.rst [skip ci] (24 hours ago) - commit 5de9b06 - (Sebastien Tourbier) * CI: update test-02 output list and re-enable to check difference (24 hours ago) - commit 75881aa - (Sebastien Tourbier) * DOC: update intro with BIDS in outputs.rst [skip ci] (24 hours ago) - commit ccb46aa - (Sebastien Tourbier) * DOC: fix bids entities table in outputs.rst [skip ci] (25 hours ago) - commit 06609b5 - (Sebastien Tourbier) * DOC: rearranged bids entities description and table in outputs.rst [skip ci] (25 hours ago) - commit b15dc08 - (Sebastien Tourbier) * DOC: update outputs.rst [skip ci] (25 hours ago) - commit 5c73f26 - (Sebastien Tourbier) * CI: update output list of test-01 (26 hours ago) - commit 125aa92 - (Sebastien Tourbier) * CI: comment check diff of test-02 outputs (26 hours ago) - commit c74e31d - (Sebastien Tourbier) * DOC: update outputs with new structure and add execution workflow PNG image (2 days ago) - commit af00c0e - (Sebastien Tourbier) * CI: updated list of outputs and uncommented difference checks (2 days ago) - commit dcfdc48 - (Sebastien Tourbier) * CI: reduce number of stacks in data/code/participants_params.json [skip ci] (2 days ago) - commit aef9b6b - (Sebastien Tourbier) * DOC: reviewed order in TOC of index.rst [skip ci] (2 days ago) - commit ba5f9aa - (Sebastien Tourbier) * DOC: renamed hamzake -> Hamza Kebiri in contributors.rst [skip ci] (2 days ago) - commit 5f101ee - (Sebastien Tourbier) * DOC: add extra blank line at end of contributors.rst [skip ci] (2 days ago) - commit 30ccd27 - (Sebastien Tourbier) * DOC: reviewed layout in contributors as it is not properly built [skip ci] (2 days ago) - commit 41775d4 - (Sebastien Tourbier) * DOC: removed versions of required python packages (2 days ago) - commit 65e4701 - (Sebastien Tourbier) * DOC: add page for contributors [skip ci] (2 days ago) - commit 20ba446 - (Sebastien Tourbier) * MAINT: correct code style issue in README [skip ci] (2 days ago) - commit 362872a - (Sebastien Tourbier) * MAINT: correct code style issue in README [skip ci] (2 days ago) - commit 7b9f644 - (Sebastien Tourbier) * MAINT: correct code style issue in README [skip ci] (2 days ago) - commit 95ffeea - (Sebastien Tourbier) * FIX: changed log_directory in srr.py (2 days ago) - commit 048d215 - (Sebastien Tourbier) * DOC: update README [skip ci] (2 days ago) - commit 421f0f9 - (Sebastien Tourbier) * DOC: update list of resources in README [skip ci] (2 days ago) - commit 4764f7c - (Sebastien Tourbier) * DOC: updated README [skip ci] (2 days ago) - commit 8b6ccfa - (Sebastien Tourbier) * DOC: add link to all contributors specification in contributing.rst [skip ci] (2 days ago) - commit ed3d75d - (Sebastien Tourbier) * DOC: add generation of PDF to .readthedocs.yml config (2 days ago) - commit 241af0f - (Sebastien Tourbier) * DOC: add missing label for reference of contributing page (2 days ago) - commit 3e33fd4 - (Sebastien Tourbier) * MAINT: should fix issues in README (2 days ago) - commit 3e2eb19 - (Sebastien Tourbier) * MAINT: fix double quote issue in build_sphinx_docs.sh (2 days ago) - commit 9ea7143 - (Sebastien Tourbier) * MAINT: remove unnecessary comments (2 days ago) - commit 771a1c4 - (Sebastien Tourbier) * MAINT: fixed indentation (2 days ago) - commit fd16d70 - (Sebastien Tourbier) * MAINT: shorten long line in srr.py (2 days ago) - commit 5714f97 - (Sebastien Tourbier) * MAINT: fix code style issues (2 days ago) - commit 09cd838 - (Sebastien Tourbier) * DOC: add docstring to get_parser() (2 days ago) - commit 8971a3b - (Sebastien Tourbier) * MAINT: fix code style and add docstrings (2 days ago) - commit 3674edd - (Sebastien Tourbier) * MAINT: Correct code style issues in dockerfile (2 days ago) - commit 1da789c - (Sebastien Tourbier) * CI: comment comparison with list of outputs before update (2 days ago) - commit 677279a - (Sebastien Tourbier) * MAINT: fix additional code style issues reported by codacy (2 days ago) - commit db35eb4 - (Sebastien Tourbier) * MAINT: fix code style issues in setup.py (2 days ago) - commit 78e2811 - (Sebastien Tourbier) * MAINT: reviewed structure of outputs for multiple reconstruction of the same subject (2 days ago) - commit 14c5c83 - (Sebastien Tourbier) * DOC: add missing docstrings (2 days ago) - commit b996b57 - (Sebastien Tourbier) * MAINT: fix a number of codacy code style issues (2 days ago) - commit 33fdb2f - (Sebastien Tourbier) * MAINT: removed unnecessary self as input of the run() function (2 days ago) - commit ca392b0 - (Sebastien Tourbier) * MAINT: update year in copyrights (2 days ago) - commit 6303781 - (Sebastien Tourbier) * DOC: update example of run() function (2 days ago) - commit 9705c17 - (Sebastien Tourbier) * DOC: fix default value of input argument cwd of the run() function (2 days ago) - commit 0356c7e - (Sebastien Tourbier) * DOC: update copyright (2 days ago) - commit 856a9de - (Sebastien Tourbier) * DOC: updated logo PNG for mialsrtk (and added SVG) where I removed C++ (2 days ago) - commit bbb8b26 - (Sebastien Tourbier) * DOC: add docstrings in utils.py (2 days ago) - commit 18bf8f9 - (Sebastien Tourbier) * DOC: update docstrings (2 days ago) - commit 3a15e99 - (Sebastien Tourbier) * DOC: removed section title in api_pipelines.rst (2 days ago) - commit e515bff - (Sebastien Tourbier) * DOC: update ABOUT the index.rst and remove link to notebook in TOC (2 days ago) - commit b523756 - (Sebastien Tourbier) * DOC: update contributing.rst (2 days ago) - commit 8108a0f - (Sebastien Tourbier) * DOC: update citing.rst (2 days ago) - commit f3136a9 - (Sebastien Tourbier) * DOC: reviewed example for anatomical pipeline (2 days ago) - commit c773500 - (Sebastien Tourbier) * DOC: reviewed docstring of anatomical pipeline (2 days ago) - commit 3ced881 - (Sebastien Tourbier) * DOC: correct docstring code style issues (2 days ago) - commit d9cbae7 - (Sebastien Tourbier) * Update conf.py (3 days ago) - commit a48c5ec - (Sébastien Tourbier) * Update requirements.txt (3 days ago) - commit f4306d1 - (Sébastien Tourbier) * Update api_preprocess.rst (3 days ago) - commit c85fa23 - (Sébastien Tourbier) * DOC: try autosummary in preprocess module (3 days ago) - commit 409b710 - (Sébastien Tourbier) * DOC: commented autodoc_default_options in conf.py (3 days ago) - commit 77272f2 - (Sébastien Tourbier) * Update .readthedocs.yml (3 days ago) - commit 5568c6e - (Sébastien Tourbier) * DOC: add summary to all autodoc directives in conf.py (3 days ago) - commit ee123a4 - (Sébastien Tourbier) * DOC: Add autodoc summary package to requirements.txt (3 days ago) - commit 3a51ebc - (Sébastien Tourbier) * FIX: Update output_SRmask -> output_srmask which caused circleci test to fail (3 days ago) - commit 096ebf1 - (Sébastien Tourbier) * DOC: Update reconstruction.py for ImageReconstruction module (3 days ago) - commit 4598dea - (Priscille) * DOC: Update reconstruction.py for MialsrtkTVSuperResolution modules. (3 days ago) - commit 4cb5528 - (Priscille) * CI: Resolved white spaces issues in post-/pre- process files. (3 days ago) - commit 6b0065f - (Priscille) * DOC: Update postprocess.py for MialsrtkN4BiasFieldCorrection modules. (3 days ago) - commit 7434c02 - (Priscille) * DOC: Update postprocess.py for MialsrtkRefineHRMaskByIntersection modules. (3 days ago) - commit fbdc612 - (Priscille) * Update .readthedocs.yml (4 days ago) - commit 1abffeb - (Sébastien Tourbier) * DOC: Update .readthedocs.yml to V2 (4 days ago) - commit 37816e1 - (Sébastien Tourbier) * DOC: add napoleon extension to sphinx config (4 days ago) - commit 973f0a2 - (Sébastien Tourbier) * Update postprocess.py (4 days ago) - commit 0f96db5 - (hamzake) * Update reconstruction.py (4 days ago) - commit 2a0a313 - (hamzake) * Update preprocess.py (4 days ago) - commit 8df484c - (hamzake) * Update srr.py (4 days ago) - commit 3d8714a - (hamzake) * Update preprocess.py (7 days ago) - commit 08e224e - (hamzake) * Update preprocess.py (7 days ago) - commit e1456c1 - (hamzake) * Update preprocess.py (7 days ago) - commit d973fa6 - (hamzake) * Merge remote-tracking branch 'origin/dev-pgd-hk' into dev-pgd-hk (7 days ago) - commit 9707aa1 - (Sebastien Tourbier) * FIX: remove typo in code line 199 that made tests in circleci failing (7 days ago) - commit d6edf0a - (Sebastien Tourbier) * Update preprocess.py (7 days ago) - commit b24e1be - (hamzake) * Update preprocess.py (7 days ago) - commit 343bb56 - (hamzake) * MAINT: fix code style issue in script reported by codacy (7 days ago) - commit e6e5ee4 - (Sebastien Tourbier) * MAINT: fix code style issue in script reported by codacy (7 days ago) - commit 89a3a7f - (Sebastien Tourbier) * DOC: add contributing page with description how to build the bidsapp and the doc locally (7 days ago) - commit 186e73a - (Sebastien Tourbier) * DOC: Correct Postprocess page title (7 days ago) - commit 7bff376 - (Priscille) * DOC: Update documentation of anatomical srr pipeline. (7 days ago) - commit b77d22c - (Priscille) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (7 days ago) - commit 0a0da2f - (Priscille) * Update brainExtractionTwoSteps.py (7 days ago) - commit e6433c6 - (hamzake) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (7 days ago) - commit 7001fa7 - (Priscille) * Update preprocess.py (7 days ago) - commit a4be1ef - (hamzake) * CI: Resolved issue on empty dictionaries (7 days ago) - commit 61a7fda - (Priscille) * DOC: Update on InputSpec and OutputSpec descriptions (7 days ago) - commit 95ac456 - (Priscille) * DOC: add skimage module to be ignore by readthedocs (7 days ago) - commit 2567fac - (Sebastien Tourbier) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (7 days ago) - commit 04f0d13 - (Priscille) * DOC: try to ignore missing modules to build doc from docstrings (7 days ago) - commit ee45cda - (Sebastien Tourbier) * DOC: Update documentation for MialsrtkIntensityStandardization, MialsrtkHistogramNormalization and MialsrtkMaskImage. (7 days ago) - commit 7ad284b - (Priscille) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (7 days ago) - commit b0c16b7 - (Priscille) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (7 days ago) - commit 23563af - (Priscille) * DOC: add files and update TOC of index with API documentation from docstrings (7 days ago) - commit 0bfb7f1 - (Sebastien Tourbier) * DOC: reviewed sphinx conf.py to browse docstrings (7 days ago) - commit d70edd2 - (Sebastien Tourbier) * DOC: Update documentation for SliceBySliceCorrectBiasField - multiple and single. (7 days ago) - commit a0b4495 - (Priscille) * Update srr.py (7 days ago) - commit 6122588 - (hamzake) * DOC: Update documentation for SliceBySliceN4BiasFieldCorrection - multiple and single. (7 days ago) - commit 0f91f7f - (Priscille) * DOC: Update documentation for SliceIntensityCorrection - multiple and single. (7 days ago) - commit 008423f - (Priscille) * Merged conflicts dev-pgd-hk (7 days ago) - commit 113fc84 - (Priscille) * DOC: Update documentation of NLM denoising - multiple and single. (7 days ago) - commit 2e0a8d0 - (Priscille) * Update installation.rst (7 days ago) - commit 2f3f15d - (hamzake) * Update preprocess.py (7 days ago) - commit 8cb4ecc - (hamzake) * CI: Resolved CI issues in bidsapp py file (7 days ago) - commit 69324b9 - (Priscille) * CI: Resolved CI issues in pymialsrtk python files (7 days ago) - commit b3c8c6b - (Priscille) * Update postprocess.py (8 days ago) - commit c3ce457 - (hamzake) * Update preprocess.py (8 days ago) - commit 77aa88c - (hamzake) * Update preprocess.py (8 days ago) - commit f690c88 - (hamzake) * Merge pull request #4 from Medical-Image-Analysis-Laboratory/dev-hk (2 weeks ago) - commit 74bb016 - (Sébastien Tourbier) * CI: Enable again to check difference of lists of outputs (2 weeks ago) - commit 98cb9a4 - (Sébastien Tourbier) * FIX: fix pyface version to 7.0.0 as pyface 7.1.0 triggered error on circleci (2 weeks ago) - commit f16619e - (Sébastien Tourbier) * CI: comment difference of output lists (2 weeks ago) - commit 74b735a - (Sébastien Tourbier) * CI: remove _id from ouput LR brain mask filenames of test-02 (2 weeks ago) - commit d94468f - (Sébastien Tourbier) * MAINT: remove _id- from brain mask filename generated by DL method (2 weeks ago) - commit 0956e0d - (Sébastien Tourbier) * CI: check difference of list of outputs for test-01 and test-02 (2 weeks ago) - commit d23c6a6 - (Sébastien Tourbier) * CI: create test-02_outputs.txt (2 weeks ago) - commit 14fb728 - (Sébastien Tourbier) * CI: update and rename test_outputs.txt to test-01_outputs.txt (2 weeks ago) - commit 8d9e91e - (Sébastien Tourbier) * CI: rename log file for each test (3 weeks ago) - commit 49cd0ee - (Sebastien Tourbier) * CI: fix name of the list of outputs for test 2 (3 weeks ago) - commit a2530a3 - (Sebastien Tourbier) * MAINT: renamed correctly brain masks in the datasinker (3 weeks ago) - commit 66aa998 - (Sebastien Tourbier) * MAINT: Delete obsolete superresolution.py (3 weeks ago) - commit 78ce8d5 - (Sebastien Tourbier) * DOC: Add new cell to brainhack.ipynb to try to integrate in the sphinx doc (3 weeks ago) - commit 04a1666 - (Sebastien Tourbier) * DOC: Add pandoc and nbsphinx to conda environment for doc generation (3 weeks ago) - commit e199927 - (Sebastien Tourbier) * DOC: Improve way to get directory of script for doc on macosx (3 weeks ago) - commit 543bb1d - (Sebastien Tourbier) * Update brainExtractionTwoSteps.py (3 weeks ago) - commit f9b891e - (hamzake) * Update preprocess.py (3 weeks ago) - commit c305d8f - (hamzake) * Update preprocess.py (4 weeks ago) - commit 196cb10 - (hamzake) * Correct brain extraction and coding style (4 weeks ago) - commit 6a4c779 - (Hamza Kebiri) * Merge branch 'dev-hk' of https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-hk (4 weeks ago) - commit c456526 - (Hamza Kebiri) * correct brain extraction to get better masks (4 weeks ago) - commit 05ad4b6 - (Hamza Kebiri) * correct brain extraction to get better masks (4 weeks ago) - commit 9054b11 - (Hamza Kebiri) * FIX: pred -> pred_ (6 weeks ago) - commit bc3c535 - (Sebastien Tourbier) * ENH: print error traceback (6 weeks ago) - commit 2efa487 - (Sebastien Tourbier) * FIX: reviewed output of enumerate() in for loop for brain extraction interface (9 weeks ago) - commit fc06344 - (Sebastien Tourbier) * DOC: added badges [skip ci] (9 weeks ago) - commit ea65487 - (Sebastien Tourbier) * MAINT: corrected extra code style issues detected by python linter (codacy) (9 weeks ago) - commit fbba4bb - (Sebastien Tourbier) * MAINT: remove useless cd .. and sudo in dockerfile (9 weeks ago) - commit a60931c - (Sebastien Tourbier) * MAINT: corrected more code style errors in Dockerfiles README and preprocess.py files (9 weeks ago) - commit 36c1c4a - (Sebastien Tourbier) * Merge remote-tracking branch 'origin/dev-hk' into dev-hk (9 weeks ago) - commit fb12e7f - (Sebastien Tourbier) * MAINT: corrected a number of code style errors reported by codacy (9 weeks ago) - commit dc97819 - (Sebastien Tourbier) * MAINT: add logo as markdown heading (9 weeks ago) - commit 1ddee82 - (Sébastien Tourbier) * MAINT: corrected code quality issues detected by linters (codacy) [skip ci] (9 weeks ago) - commit 26bc8c7 - (Sebastien Tourbier) * MAINT: corrected code quality issues detected by linters (codacy) (9 weeks ago) - commit f3bab65 - (Sebastien Tourbier) * Merge pull request #16 from Medical-Image-Analysis-Laboratory/dev-pgd-hk (9 weeks ago) - commit b6cce53 - (Sébastien Tourbier) * CI: add test with automatic brain extraction (9 weeks ago) - commit 376a91f - (Sebastien Tourbier) * CI: add missing orb for codacy reporter (9 weeks ago) - commit 1fd19d8 - (Sebastien Tourbier) * ENH: enable nipype to generate provenance report (9 weeks ago) - commit 2924772 - (Sebastien Tourbier) * CI: add job that sends coverage report to codacy in workflow (9 weeks ago) - commit dbe5c75 - (Sebastien Tourbier) * MAINT: remove unwanted crash files [skip ci] (9 weeks ago) - commit dff8864 - (Sebastien Tourbier) * CI: fix missing - run: (9 weeks ago) - commit 26ab5e2 - (Sebastien Tourbier) * CI: updated test job for code coverage and send coverage report to codacy (9 weeks ago) - commit e53e248 - (Sebastien Tourbier) * CI: store artifacts for code coverage on circleci (9 weeks ago) - commit 3ca0638 - (Sebastien Tourbier) * ENH: add code coverage (9 weeks ago) - commit 659a6fc - (Sebastien Tourbier) * Updated BrainExtractionTwoSteps.py to be conform to brain extraction changes in preprocess.py (2 months ago) - commit 199fd2d - (Hamza Kebiri) * Corrected bug where masks were not saved in the right location and hence the following nodes were wrongly working (2 months ago) - commit d394ad3 - (Hamza Kebiri) * MAINT: upgrade Nipype to 1.5.1 (2 months ago) - commit b4945a1 - (Sebastien Tourbier) * FIX: remove capture_output from run and print interface exception during exec (2 months ago) - commit 57cc0b5 - (Sebastien Tourbier) * Update preprocess.py (2 months ago) - commit ff8f056 - (hamzake) * Adapt other scripts (preprocess.py mainly) to be compatible with brain extraction in two steps and correct bugs (2 months ago) - commit 0018f02 - (Hamza Kebiri) * Merge branch 'dev-hk' of https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-hk (3 months ago) - commit edd2281 - (Hamza Kebiri) * Replace current one shot segmentation with two-steps (localization + segmentation), Include checkpoints corresponding to networks trained with WithoutEyesTrain dataset (biggest dataset) (3 months ago) - commit 2942caa - (Hamza Kebiri) * FIX: make run possible if tensorflow failed but manual mask are used (4 months ago) - commit 044a025 - (Sebastien Tourbier) * CI: update docker run command with flag --manual (4 months ago) - commit 0de2a0c - (Sebastien Tourbier) * Remove duplicated run.py bidsapp code (4 months ago) - commit 258f212 - (Sebastien Tourbier) * Add missing untracked file (4 months ago) - commit 7b86221 - (Sebastien Tourbier) * FIX: update dockerfile and add missing untracked files (4 months ago) - commit d7b2ef2 - (Sebastien Tourbier) * ENH: add new parser input flag '--manual' (4 months ago) - commit 45d9f98 - (Sebastien Tourbier) * ENH: add code for brain extraction (4 months ago) - commit 1e4a897 - (Sebastien Tourbier) * Add channel anaconda to environment of jupyter image (4 months ago) - commit cfe5284 - (Sebastien Tourbier) * Update notebook (4 months ago) - commit 24e509f - (Sebastien Tourbier) * CONDA: reviewed list of packages to be installed (add packages for brainextraction) (4 months ago) - commit 451a152 - (Sebastien Tourbier) * ENH: add coverage in docker (4 months ago) - commit 8b7b27a - (Sebastien Tourbier) * MAINT: moved code (4 months ago) - commit 31fb4dd - (Sebastien Tourbier) * DOCKER: update to miniconda3 (4 months ago) - commit b1df0a5 - (Sebastien Tourbier) * MAINT: do not ignore content of docker folder by dockerfile (4 months ago) - commit 168a5cb - (Sebastien Tourbier) * DOC: update toc in index page with outputs page (5 months ago) - commit 69c920d - (Sébastien Tourbier) * DOC: create outputs.rst (5 months ago) - commit 78c570b - (Sébastien Tourbier) * DOC: update badge for readthedocs (5 months ago) - commit 11337e8 - (Sébastien Tourbier) * DOC: update badge (5 months ago) - commit 268d4b5 - (Sébastien Tourbier) * MAINT: updated badges in readthedocs (5 months ago) - commit d81fad8 - (Sébastien Tourbier) * MAINT: fix typo in badge (5 months ago) - commit cdb8532 - (Sébastien Tourbier) * MAINT: updated badges in readme (5 months ago) - commit ec8af9f - (Sébastien Tourbier) * Bugs correction and inclusion of PGD post-processing of binarized network outputs using mathematical morphology (5 months ago) - commit 3da12d1 - (Hamza Kebiri) * Merge pull request #15 from Medical-Image-Analysis-Laboratory/dev-pgd-hk (5 months ago) - commit c0b0645 - (Sébastien Tourbier) * MAINT: created get_parser() function (5 months ago) - commit f02e9cc - (Sébastien Tourbier) * MAINT: add shebang (5 months ago) - commit 01041b3 - (Sébastien Tourbier) * remove checkpoint from wrong old location (5 months ago) - commit 064a082 - (Hamza Kebiri) * change location of network checkpoint for brain extraction to pymialsrtk/data (5 months ago) - commit 58404f8 - (Hamza Kebiri) * Merge pull request #14 from Medical-Image-Analysis-Laboratory/master (5 months ago) - commit 1fa9e64 - (Sébastien Tourbier) * Merge pull request #13 from Medical-Image-Analysis-Laboratory/all-contributors/add-meribach (5 months ago) - commit ede6824 - (Sébastien Tourbier) * Merge branch 'master' into all-contributors/add-meribach (5 months ago) - commit d3e72c9 - (Sébastien Tourbier) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit 4c15cca - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit feee7d3 - (allcontributors[bot]) * Merge pull request #12 from Medical-Image-Analysis-Laboratory/all-contributors/add-hamzake (5 months ago) - commit 8d4eefd - (Sébastien Tourbier) * Merge branch 'master' into all-contributors/add-hamzake (5 months ago) - commit ba7d6ac - (Sébastien Tourbier) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit 08aef83 - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit cd5763c - (allcontributors[bot]) * Merge pull request #11 from Medical-Image-Analysis-Laboratory/all-contributors/add-pdedumast (5 months ago) - commit 48d74bd - (Sébastien Tourbier) * Merge branch 'master' into all-contributors/add-pdedumast (5 months ago) - commit 1c2f6f8 - (Sébastien Tourbier) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit a043dfe - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit 7bdb182 - (allcontributors[bot]) * Merge pull request #6 from Medical-Image-Analysis-Laboratory/all-contributors/add-sebastientourbier (5 months ago) - commit 7e040f8 - (Sébastien Tourbier) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit 93dadca - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit ffc6280 - (allcontributors[bot]) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit f7256f7 - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit 3f34d68 - (allcontributors[bot]) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit b7d4b5c - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit 5b62e73 - (allcontributors[bot]) * docs: update .all-contributorsrc [skip ci] (5 months ago) - commit 513bd8e - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit fdb4d12 - (allcontributors[bot]) * Update README.md (5 months ago) - commit 78ec47b - (Sébastien Tourbier) * Update README.md (5 months ago) - commit 54d4b0c - (Sébastien Tourbier) * Merge pull request #5 from Medical-Image-Analysis-Laboratory/all-contributors/add-sebastientourbier (5 months ago) - commit 6fbe9d8 - (Sébastien Tourbier) * docs: create .all-contributorsrc [skip ci] (5 months ago) - commit c738d32 - (allcontributors[bot]) * docs: update README.md [skip ci] (5 months ago) - commit ad4b950 - (allcontributors[bot]) * DOC: improved content (5 months ago) - commit 812cd33 - (Sebastien Tourbier) * FIX: imports for parser (5 months ago) - commit 0fc42e8 - (Sebastien Tourbier) * DOC: fix link to config schema (5 months ago) - commit fc0e8ce - (Sebastien Tourbier) * DOC: improve page on BIDS and BIDS App (5 months ago) - commit 84bccfe - (Sebastien Tourbier) * FIX: parser in doc (5 months ago) - commit 170d9e7 - (Sebastien Tourbier) * FIX: added parser.py (5 months ago) - commit 4ab297c - (Sebastien Tourbier) * FIX: reviewed parser structure (5 months ago) - commit aa45bd3 - (Sebastien Tourbier) * FIX: missing __init__.py for pipelines.anatomical module (5 months ago) - commit 804f57b - (Sebastien Tourbier) * DOC: fix nbsphinx version (5 months ago) - commit 18e172b - (Sebastien Tourbier) * DOC: added the brainhack notebook as example [skip ci] (5 months ago) - commit 9c535a5 - (Sebastien Tourbier) * DOC: add example of notebook [skip ci] (5 months ago) - commit 3ff3ec0 - (Sebastien Tourbier) * DOC: added pip requirements.txt for readthedocs (5 months ago) - commit 1ef3114 - (Sebastien Tourbier) * DOC: added .readthedocs.yml (5 months ago) - commit 1afdf27 - (Sebastien Tourbier) * DOC: created sphinx doc for BIDS App to be later published on readthedocs [skip ci] (5 months ago) - commit 79b0830 - (Sebastien Tourbier) * FIX: added anatomical to setup.py packages (5 months ago) - commit c633e0e - (Sebastien Tourbier) * MAINT: update default param_file in parser (5 months ago) - commit c1d30a9 - (Sebastien Tourbier) * ENH: ignore _build folder by git (5 months ago) - commit f202b76 - (Sebastien Tourbier) * CI: enabled comparison of lists of outputs (5 months ago) - commit 7b9b7c5 - (Sebastien Tourbier) * CI: added list of output files for test (5 months ago) - commit 3910c26 - (Sebastien Tourbier) * MAINT: update docker image metadata (5 months ago) - commit dd34ea8 - (Sebastien Tourbier) * CI: fix wrong path (5 months ago) - commit fcdc245 - (Sebastien Tourbier) * CI: fix missing removed reference to cmp3 + typos (5 months ago) - commit 3dc0d50 - (Sebastien Tourbier) * CI: removed all references to get_data (5 months ago) - commit 6a797e9 - (Sebastien Tourbier) * CI: test (5 months ago) - commit 346aff6 - (Sebastien Tourbier) * ENH: add config for continuous integration testing with circleci (5 months ago) - commit 669df35 - (Sebastien Tourbier) * ENH: generate colored PNG of the graph (5 months ago) - commit 229bed1 - (Sebastien Tourbier) * FIX: reviewed outputs sinked to anat folder (5 months ago) - commit d75c66f - (Sebastien Tourbier) * FIX: rename data and json sinkers (5 months ago) - commit ecd6ffd - (Sebastien Tourbier) * FIX: rename workflow base dir (impossible with only `int`, data sinker always create anat/_1 if we use _1) (5 months ago) - commit b631db1 - (Sebastien Tourbier) * FIX: install missing graphviz and pydotplus for saving PNG of graph (5 months ago) - commit 3121640 - (Sebastien Tourbier) * MAINT: change stack order (same as script) (5 months ago) - commit 5f03b8c - (Sebastien Tourbier) * FIX: reviewed datasink node (5 months ago) - commit 680fc87 - (Sebastien Tourbier) * FIX: added graphviz otherwise missing module dot for generation of graph (I guess) (5 months ago) - commit 7cc8f59 - (Sebastien Tourbier) * FIX: make output BIDS compliant (except for id-<label>) (5 months ago) - commit fbea548 - (Sebastien Tourbier) * FIX: update pipeline output dir and fix int -> str conversion (5 months ago) - commit a9e8924 - (Sebastien Tourbier) * ENH: get __version__` from `info.py` (5 months ago) - commit 58c60df - (Sebastien Tourbier) * MAINT: update version (5 months ago) - commit cec5477 - (Sebastien Tourbier) * FIX: downgrade version of numpy installed (5 months ago) - commit 3344176 - (Sebastien Tourbier) * ENH: update dockerfile to create the BIDS App (5 months ago) - commit 655c1af - (Sebastien Tourbier) * MAINT: deleted line (5 months ago) - commit e6afc8e - (Sebastien Tourbier) * FIX: corrected field `sr-id` with respect to `srr.py` (5 months ago) - commit ad70f57 - (Sebastien Tourbier) * MAINT: corrected typo (5 months ago) - commit 05185a5 - (Sebastien Tourbier) * MAINT: added new derivatives folders to be ignored (5 months ago) - commit 7cf2817 - (Sebastien Tourbier) * FIX: Typo in directory path (5 months ago) - commit 7e50451 - (Priscille) * STYLE: Ouptut directory architecture. SR id parameters is now mandatory. (5 months ago) - commit b294b7a - (Priscille) * STYLE: Add version file (5 months ago) - commit 4233f6b - (Priscille) * STYLE: Modified final result filenames (5 months ago) - commit 668b278 - (Priscille) * STYLE: Super-resolution id as string (5 months ago) - commit 319619c - (Priscille) * Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit into dev-pgd-hk (5 months ago) - commit e2875ee - (Priscille) * ENH: super-resolution reconstruction pipeline script + demo parameters json file (5 months ago) - commit 9cbd622 - (Priscille) * Add automatic brain extraction with U-Net (5 months ago) - commit 213e123 - (Hamza Kebiri) * ENH: added network checkpoint for brain extraction after training (5 months ago) - commit 99bbb83 - (Hamza Kebiri) * ENH: added .gitattributes for managing checkpoint file with git LFS (5 months ago) - commit bc396e1 - (Hamza Kebiri) * ENH: Use of DataSinker node to save final results (5 months ago) - commit b130576 - (Priscille) * Merge pull request #3 from Medical-Image-Analysis-Laboratory/master (5 months ago) - commit 4678488 - (Sébastien Tourbier) * Update README.md (5 months ago) - commit 060512b - (Sébastien Tourbier) * ENH: Working SRR pipeline and clean interfaces (5 months ago) - commit c4fbabf - (Priscille) * ENH: Updates on SRR pipeline (5 months ago) - commit ecaa16d - (Priscille) * Working srr pipeline (10 months ago) - commit a430a80 - (Priscille) * BUG & STYLE: Fixed nipype nodes & Separation of preprocessing and reconstruction modules (10 months ago) - commit 09cb903 - (Priscille) * ENH: Complete SRR pipeline (10 months ago) - commit e5dd36e - (Priscille) * BUG: Fixed final nipype node N4biasFieldCorrection (10 months ago) - commit d4e92fe - (Priscille) * ENH: Specification of stacks order in most of the nipype nodes (10 months ago) - commit a03b0d9 - (Priscille) * ENH: Development of final nipype nodes + integration to pipeline (10 months ago) - commit 8ff81d5 - (Priscille) * BUG-ENH: Fixed mialsrtkHistogramNormalization and mialsrtkIntensityStandardization. Addition of mialsrtkImageReconstruction and addition to srr workflow (10 months ago) - commit b3fe6b7 - (Priscille) * ENH: Updated nipype node MialsrtkIntensityStandardization + integration to preprocessing workflow (10 months ago) - commit 7e7f12e - (Priscille) * ENH: Added nipype node MialsrtkSliceBySliceCorrectBiasField + integration to preprocessing workflow (10 months ago) - commit 467bdd2 - (Priscille) * ENH: SRR preprocessing workflow - NLM denoising and Slice intensity correction (10 months ago) - commit adb8b40 - (Priscille) * BUG: Fixed output directory of BtkNLMDenoising (10 months ago) - commit a1d377f - (Priscille) * STYLE: Remove crash files (10 months ago) - commit 11f038e - (Priscille) * Merge branch 'dev-hk' into dev-pgd-hk (10 months ago) - commit ad50a20 - (Priscille) * orientImage is ok, superResolution finishes but does not generate SR images, histogramNormalization skeleton is done but the .py file running behind is not successfully ran due to a version problem, brainExtraction is ongoing (1 year ago) - commit 77253ec - (Hamza Kebiri) * ENH: Development of nope MialsrtkImageReconstruction. NOT tested! (1 year, 1 month ago) - commit c0a1a85 - (Priscille) * ENH: Updated nipype node MialsrtkIntensityStandardization for customized parameters (1 year, 1 month ago) - commit 4115548 - (Priscille) * ENH: Added nipype node MialsrtkIntensityStandardization (1 year, 1 month ago) - commit 7c33b87 - (Priscille) * ENH: Added nipype node MialsrtkSliceBySliceN4BiasFieldCorrection (1 year, 1 month ago) - commit 8861ca7 - (Priscille) * ENH: Added nipype node MialsrtkCorrectSliceIntensity (1 year, 1 month ago) - commit 6793ca5 - (Priscille) * ENH: Updated notebook (1 year, 2 months ago) - commit 92048dd - (Sebastien Tourbier) * MAINT: removed line sub-01 ses-02 0.75 0.01 (1 year, 2 months ago) - commit cc2dd6d - (Sebastien Tourbier) * Merge branch 'dev' of github.com:sebastientourbier/mialsuperresolutiontoolkit into dev (1 year, 2 months ago) - commit f08a1a8 - (Sebastien Tourbier) * ENH: added source code and notebook for pymialsrtk (1 year, 2 months ago) - commit 47ed624 - (Sebastien Tourbier) * ENH: ignore __pycache__ generated by pymialsrtk at install (python setup.py install) (1 year, 2 months ago) - commit 5e88343 - (Sebastien Tourbier) * ENH: reviewed docker image build and added docker image with jupyter notebook for prototype development (1 year, 2 months ago) - commit 18f7898 - (Sebastien Tourbier) * ENH: git ignores ipython notebook checkpoints (1 year, 2 months ago) - commit 091d476 - (Sebastien Tourbier) * FIX: updated dataset_description.json according to pybids 0.9.1 (1 year, 2 months ago) - commit 9bcff58 - (Sebastien Tourbier) * TST: updated batch_list.txt with new case to be processed (1 year, 3 months ago) - commit 42f6fe5 - (Sébastien Tourbier) * FIX: added condition for detecting linux or Mac OS (1 year, 3 months ago) - commit 5be1fed - (sebastientourbier) * CI: removed old travis.yml config file (1 year, 3 months ago) - commit 9ea2a81 - (sebastientourbier) * MAINT: updated version tag (1 year, 3 months ago) - commit 2f007a6 - (Sebastien Tourbier) * ENH: reviewed testing dataset (BIDS) and made the main pipeline script execution more generic (1 year, 3 months ago) - commit e0af3b5 - (Sebastien Tourbier) * ENH: reviewed testing dataset and main pipeline script execution, taking a BIDS dataset as input (1 year, 3 months ago) - commit d6a3264 - (Sebastien Tourbier) * Fix version release to use in the demo batch script (1 year, 6 months ago) - commit ee3cd2c - (Sebastien Tourbier) * SAMPLE DATA: new BIDS json sidecar for brain masks (1 year, 6 months ago) - commit dde642f - (Sebastien Tourbier) * FIX: filename typos + extra line in list of scans (1 year, 6 months ago) - commit d643809 - (Sebastien Tourbier) * SAMPLE DATA: updated BIDS datasets and required files (1 year, 6 months ago) - commit b520fc3 - (Sebastien Tourbier) * SAMPLE DATA: Removed files and updated BIDS dataset (1 year, 6 months ago) - commit 64bc529 - (Sebastien Tourbier) * Creation of scripts to generate BIDS derivatives json sidecar (1 year, 6 months ago) - commit 5ec8afe - (Sebastien Tourbier) * Added some derivatives folder ignored by git (1 year, 6 months ago) - commit 97918a5 - (Sebastien Tourbier) * FIX: dataset sample scripts (1 year, 6 months ago) - commit 19c7fec - (Sebastien Tourbier) * DOC: updated tutorial to use docker (1 year, 6 months ago) - commit 6b72e54 - (Sebastien Tourbier) * Added Xavier to Zenodo (1 year, 6 months ago) - commit 46fc34f - (Sebastien Tourbier) * Deleted some data derivatives (1 year, 6 months ago) - commit f77f9f4 - (Sebastien Tourbier) * FIX: typo in superresolution_pipeline.sh (1 year, 6 months ago) - commit a64faf9 - (Sebastien Tourbier) * Files/Structure for the new testing dataset (1 year, 6 months ago) - commit 26eeacc - (Sebastien Tourbier) * ENH: Updated testing data structure / Dockerfile / superresolution scripts (1 year, 6 months ago) - commit cb4b4b3 - (Sebastien Tourbier) * ENH: Refactored code to take multiple inputs using argparse. Removed hard-coded glob (1 year, 6 months ago) - commit 2ee2246 - (Sebastien Tourbier) * Update README.md (1 year, 8 months ago) - commit e770896 - (Sébastien Tourbier)
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