Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

MIAL Super-Resolution Toolkit v2.0 #2

Merged
merged 336 commits into from
Nov 6, 2020
Merged

MIAL Super-Resolution Toolkit v2.0 #2

merged 336 commits into from
Nov 6, 2020
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 13, 2020

  1. CI: added list of output files for test

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    3910c26 View commit details
    Browse the repository at this point in the history

  2. CI: enabled comparison of lists of outputs

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    7b9b7c5 View commit details
    Browse the repository at this point in the history

  3. ENH: ignore _build folder by git

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    f202b76 View commit details
    Browse the repository at this point in the history

  4. MAINT: update default param_file in parser

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    c1d30a9 View commit details
    Browse the repository at this point in the history

  5. FIX: added anatomical to setup.py packages

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    c633e0e View commit details
    Browse the repository at this point in the history

  6. DOC: created sphinx doc for BIDS App to be later published on readthe… 

    …docs [skip ci]
    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    79b0830 View commit details
    Browse the repository at this point in the history

  7. DOC: added .readthedocs.yml

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    1afdf27 View commit details
    Browse the repository at this point in the history

  8. DOC: added pip requirements.txt for readthedocs

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    1ef3114 View commit details
    Browse the repository at this point in the history

  9. DOC: add example of notebook [skip ci]

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    3ff3ec0 View commit details
    Browse the repository at this point in the history

  10. DOC: added the brainhack notebook as example [skip ci]

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    9c535a5 View commit details
    Browse the repository at this point in the history

  11. DOC: fix nbsphinx version

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    18e172b View commit details
    Browse the repository at this point in the history

  12. FIX: missing __init__.py for pipelines.anatomical module

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    804f57b View commit details
    Browse the repository at this point in the history

  13. FIX: reviewed parser structure

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    aa45bd3 View commit details
    Browse the repository at this point in the history

  14. FIX: added parser.py

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    4ab297c View commit details
    Browse the repository at this point in the history

  15. FIX: parser in doc

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    170d9e7 View commit details
    Browse the repository at this point in the history

  16. DOC: improve page on BIDS and BIDS App

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    84bccfe View commit details
    Browse the repository at this point in the history

  17. DOC: fix link to config schema

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    fc0e8ce View commit details
    Browse the repository at this point in the history

  18. FIX: imports for parser

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    0fc42e8 View commit details
    Browse the repository at this point in the history

  19. DOC: improved content

    @sebastientourbier
    sebastientourbier committed Jun 13, 2020
    Configuration menu
    Copy the full SHA
    812cd33 View commit details
    Browse the repository at this point in the history

Commits on Jun 22, 2020

  1. Merge pull request #14 from Medical-Image-Analysis-Laboratory/master 

    Add contributors
    @sebastientourbier
    sebastientourbier authored Jun 22, 2020
    Configuration menu
    Copy the full SHA
    1fa9e64 View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2020

  1. change location of network checkpoint for brain extraction to pymials… 

    …rtk/data
    Hamza Kebiri committed Jun 23, 2020
    Configuration menu
    Copy the full SHA
    58404f8 View commit details
    Browse the repository at this point in the history

  2. remove checkpoint from wrong old location

    Hamza Kebiri committed Jun 23, 2020
    Configuration menu
    Copy the full SHA
    064a082 View commit details
    Browse the repository at this point in the history

  3. MAINT: add shebang

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    01041b3 View commit details
    Browse the repository at this point in the history

  4. MAINT: created get_parser() function

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    f02e9cc View commit details
    Browse the repository at this point in the history

  5. Merge pull request #15 from Medical-Image-Analysis-Laboratory/dev-pgd-hk 

    Update dev-hk branch with BIDS App changes in dev-pdg-hk branch
    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    c0b0645 View commit details
    Browse the repository at this point in the history

  6. Bugs correction and inclusion of PGD post-processing of binarized net… 

    …work outputs using mathematical morphology
    Hamza Kebiri committed Jun 23, 2020
    Configuration menu
    Copy the full SHA
    3da12d1 View commit details
    Browse the repository at this point in the history

  7. MAINT: updated badges in readme

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    ec8af9f View commit details
    Browse the repository at this point in the history

  8. MAINT: fix typo in badge

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    cdb8532 View commit details
    Browse the repository at this point in the history

  9. MAINT: updated badges in readthedocs

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    d81fad8 View commit details
    Browse the repository at this point in the history

  10. DOC: update badge

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    268d4b5 View commit details
    Browse the repository at this point in the history

  11. DOC: update badge for readthedocs

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    11337e8 View commit details
    Browse the repository at this point in the history

  12. DOC: create outputs.rst

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    78c570b View commit details
    Browse the repository at this point in the history

  13. DOC: update toc in index page with outputs page

    @sebastientourbier
    sebastientourbier authored Jun 23, 2020
    Configuration menu
    Copy the full SHA
    69c920d View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2020

  1. MAINT: do not ignore content of docker folder by dockerfile

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    168a5cb View commit details
    Browse the repository at this point in the history

  2. DOCKER: update to miniconda3

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    b1df0a5 View commit details
    Browse the repository at this point in the history

  3. MAINT: moved code

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    31fb4dd View commit details
    Browse the repository at this point in the history

  4. ENH: add coverage in docker

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    8b7b27a View commit details
    Browse the repository at this point in the history

  5. CONDA: reviewed list of packages to be installed (add packages for br… 

    …ainextraction)
    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    451a152 View commit details
    Browse the repository at this point in the history

  6. Update notebook

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    24e509f View commit details
    Browse the repository at this point in the history

  7. Add channel anaconda to environment of jupyter image

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    cfe5284 View commit details
    Browse the repository at this point in the history

  8. ENH: add code for brain extraction

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    1e4a897 View commit details
    Browse the repository at this point in the history

  9. ENH: add new parser input flag '--manual'

    @sebastientourbier
    sebastientourbier committed Jun 29, 2020
    Configuration menu
    Copy the full SHA
    45d9f98 View commit details
    Browse the repository at this point in the history

Commits on Jul 10, 2020

  1. FIX: update dockerfile and add missing untracked files

    @sebastientourbier
    sebastientourbier committed Jul 10, 2020
    Configuration menu
    Copy the full SHA
    d7b2ef2 View commit details
    Browse the repository at this point in the history

  2. Add missing untracked file

    @sebastientourbier
    sebastientourbier committed Jul 10, 2020
    Configuration menu
    Copy the full SHA
    7b86221 View commit details
    Browse the repository at this point in the history

  3. Remove duplicated run.py bidsapp code

    @sebastientourbier
    sebastientourbier committed Jul 10, 2020
    Configuration menu
    Copy the full SHA
    258f212 View commit details
    Browse the repository at this point in the history

  4. CI: update docker run command with flag --manual

    @sebastientourbier
    sebastientourbier committed Jul 10, 2020
    Configuration menu
    Copy the full SHA
    0de2a0c View commit details
    Browse the repository at this point in the history

Commits on Jul 20, 2020

  1. FIX: make run possible if tensorflow failed but manual mask are used

    @sebastientourbier
    sebastientourbier committed Jul 20, 2020
    Configuration menu
    Copy the full SHA
    044a025 View commit details
    Browse the repository at this point in the history

Commits on Aug 19, 2020

  1. Replace current one shot segmentation with two-steps (localization + … 

    …segmentation), Include checkpoints corresponding to networks trained with WithoutEyesTrain dataset (biggest dataset)
    Hamza Kebiri committed Aug 19, 2020
    Configuration menu
    Copy the full SHA
    2942caa View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev-hk' of https://github.com/Medical-Image-Analysis-La… 

    …boratory/mialsuperresolutiontoolkit into dev-hk
    Hamza Kebiri committed Aug 19, 2020
    Configuration menu
    Copy the full SHA
    edd2281 View commit details
    Browse the repository at this point in the history

Commits on Aug 24, 2020

  1. Adapt other scripts (preprocess.py mainly) to be compatible with brai… 

    …n extraction in two steps and correct bugs
    Hamza Kebiri committed Aug 24, 2020
    Configuration menu
    Copy the full SHA
    0018f02 View commit details
    Browse the repository at this point in the history

  2. Update preprocess.py

    @hamzake
    hamzake authored Aug 24, 2020
    Configuration menu
    Copy the full SHA
    ff8f056 View commit details
    Browse the repository at this point in the history

Commits on Aug 26, 2020

  1. FIX: remove capture_output from run and print interface exception dur… 

    …ing exec
    @sebastientourbier
    sebastientourbier committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    57cc0b5 View commit details
    Browse the repository at this point in the history

  2. MAINT: upgrade Nipype to 1.5.1

    @sebastientourbier
    sebastientourbier committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    b4945a1 View commit details
    Browse the repository at this point in the history

  3. Corrected bug where masks were not saved in the right location and he… 

    …nce the following nodes were wrongly working
    Hamza Kebiri committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    d394ad3 View commit details
    Browse the repository at this point in the history

  4. Updated BrainExtractionTwoSteps.py to be conform to brain extraction … 

    …changes in preprocess.py
    Hamza Kebiri committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    199fd2d View commit details
    Browse the repository at this point in the history

Commits on Sep 1, 2020

  1. ENH: add code coverage

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    659a6fc View commit details
    Browse the repository at this point in the history

  2. CI: store artifacts for code coverage on circleci

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    3ca0638 View commit details
    Browse the repository at this point in the history

  3. CI: updated test job for code coverage and send coverage report to co… 

    …dacy
    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    e53e248 View commit details
    Browse the repository at this point in the history

  4. CI: fix missing - run:

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    26ab5e2 View commit details
    Browse the repository at this point in the history

  5. MAINT: remove unwanted crash files [skip ci]

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    dff8864 View commit details
    Browse the repository at this point in the history

  6. CI: add job that sends coverage report to codacy in workflow

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    dbe5c75 View commit details
    Browse the repository at this point in the history

  7. ENH: enable nipype to generate provenance report

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    2924772 View commit details
    Browse the repository at this point in the history

  8. CI: add missing orb for codacy reporter

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    1fd19d8 View commit details
    Browse the repository at this point in the history

  9. CI: add test with automatic brain extraction

    @sebastientourbier
    sebastientourbier committed Sep 1, 2020
    Configuration menu
    Copy the full SHA
    376a91f View commit details
    Browse the repository at this point in the history

Commits on Sep 2, 2020

  1. Merge pull request #16 from Medical-Image-Analysis-Laboratory/dev-pgd-hk 

    Update dev-hk branch with changes in dev-pgd-hk:
* Update badge for badges in doc and readme
* Create the list of main outputs of the BIDS App
    @sebastientourbier
    sebastientourbier authored Sep 2, 2020
    Configuration menu
    Copy the full SHA
    b6cce53 View commit details
    Browse the repository at this point in the history

  2. MAINT: corrected code quality issues detected by linters (codacy)

    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    f3bab65 View commit details
    Browse the repository at this point in the history

  3. MAINT: corrected code quality issues detected by linters (codacy) [sk… 

    …ip ci]
    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    26bc8c7 View commit details
    Browse the repository at this point in the history

  4. MAINT: add logo as markdown heading

    @sebastientourbier
    sebastientourbier authored Sep 2, 2020
    Configuration menu
    Copy the full SHA
    1ddee82 View commit details
    Browse the repository at this point in the history

  5. MAINT: corrected a number of code style errors reported by codacy

    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    dc97819 View commit details
    Browse the repository at this point in the history

  6. Merge remote-tracking branch 'origin/dev-hk' into dev-hk

    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    fb12e7f View commit details
    Browse the repository at this point in the history

  7. MAINT: corrected more code style errors in Dockerfiles README and pre… 

    …process.py files
    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    36c1c4a View commit details
    Browse the repository at this point in the history

  8. MAINT: remove useless cd .. and sudo in dockerfile

    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    a60931c View commit details
    Browse the repository at this point in the history

  9. MAINT: corrected extra code style issues detected by python linter (c… 

    …odacy)
    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    fbba4bb View commit details
    Browse the repository at this point in the history

  10. DOC: added badges [skip ci]

    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    ea65487 View commit details
    Browse the repository at this point in the history

  11. FIX: reviewed output of enumerate() in for loop for brain extraction … 

    …interface
    @sebastientourbier
    sebastientourbier committed Sep 2, 2020
    Configuration menu
    Copy the full SHA
    fc06344 View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2020

  1. ENH: print error traceback

    @sebastientourbier
    sebastientourbier committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    2efa487 View commit details
    Browse the repository at this point in the history

  2. FIX: pred -> pred_

    @sebastientourbier
    sebastientourbier committed Sep 22, 2020
    Configuration menu
    Copy the full SHA
    bc3c535 View commit details
    Browse the repository at this point in the history

Commits on Oct 9, 2020

  1. correct brain extraction to get better masks

    Hamza Kebiri committed Oct 9, 2020
    Configuration menu
    Copy the full SHA
    9054b11 View commit details
    Browse the repository at this point in the history

  2. correct brain extraction to get better masks

    Hamza Kebiri committed Oct 9, 2020
    Configuration menu
    Copy the full SHA
    05ad4b6 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev-hk' of https://github.com/Medical-Image-Analysis-La… 

    …boratory/mialsuperresolutiontoolkit into dev-hk
    Hamza Kebiri committed Oct 9, 2020
    Configuration menu
    Copy the full SHA
    c456526 View commit details
    Browse the repository at this point in the history

Commits on Oct 12, 2020

  1. Correct brain extraction and coding style

    Hamza Kebiri committed Oct 12, 2020
    Configuration menu
    Copy the full SHA
    6a4c779 View commit details
    Browse the repository at this point in the history

  2. Update preprocess.py 

    Delete unused variable centroids and a white space (detected by app.codacy)
    @hamzake
    hamzake authored Oct 12, 2020
    Configuration menu
    Copy the full SHA
    196cb10 View commit details
    Browse the repository at this point in the history

Commits on Oct 13, 2020

  1. Update preprocess.py 

    Change 'out_postfix' from '_brainMask' to  '_masked'
    @hamzake
    hamzake authored Oct 13, 2020
    Configuration menu
    Copy the full SHA
    c305d8f View commit details
    Browse the repository at this point in the history

  2. Update brainExtractionTwoSteps.py 

    make BrainExtractionTwoSteps.py similar to brain extraction in preprocess.py
    @hamzake
    hamzake authored Oct 13, 2020
    Configuration menu
    Copy the full SHA
    f9b891e View commit details
    Browse the repository at this point in the history

Commits on Oct 19, 2020

  1. DOC: Improve way to get directory of script for doc on macosx

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    543bb1d View commit details
    Browse the repository at this point in the history

  2. DOC: Add pandoc and nbsphinx to conda environment for doc generation

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    e199927 View commit details
    Browse the repository at this point in the history

  3. DOC: Add new cell to brainhack.ipynb to try to integrate in the sphin… 

    …x doc
    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    04a1666 View commit details
    Browse the repository at this point in the history

  4. MAINT: Delete obsolete superresolution.py

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    78ce8d5 View commit details
    Browse the repository at this point in the history

  5. MAINT: renamed correctly brain masks in the datasinker

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    66aa998 View commit details
    Browse the repository at this point in the history

  6. CI: fix name of the list of outputs for test 2

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    a2530a3 View commit details
    Browse the repository at this point in the history

  7. CI: rename log file for each test

    @sebastientourbier
    sebastientourbier committed Oct 19, 2020
    Configuration menu
    Copy the full SHA
    49cd0ee View commit details
    Browse the repository at this point in the history

Commits on Oct 20, 2020

  1. CI: update and rename test_outputs.txt to test-01_outputs.txt

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    8d9e91e View commit details
    Browse the repository at this point in the history

  2. CI: create test-02_outputs.txt

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    14fb728 View commit details
    Browse the repository at this point in the history

  3. CI: check difference of list of outputs for test-01 and test-02

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    d23c6a6 View commit details
    Browse the repository at this point in the history

  4. MAINT: remove _id- from brain mask filename generated by DL method

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    0956e0d View commit details
    Browse the repository at this point in the history

  5. CI: remove _id from ouput LR brain mask filenames of test-02

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    d94468f View commit details
    Browse the repository at this point in the history

  6. CI: comment difference of output lists

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    74b735a View commit details
    Browse the repository at this point in the history

  7. FIX: fix pyface version to 7.0.0 as pyface 7.1.0 triggered error on c… 

    …ircleci
    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    f16619e View commit details
    Browse the repository at this point in the history

  8. CI: Enable again to check difference of lists of outputs

    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    98cb9a4 View commit details
    Browse the repository at this point in the history

  9. Merge pull request #4 from Medical-Image-Analysis-Laboratory/dev-hk 

    Integration of automatic DL-based brain extraction
    @sebastientourbier
    sebastientourbier authored Oct 20, 2020
    Configuration menu
    Copy the full SHA
    74bb016 View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2020

  1. Update preprocess.py 

    Add documentation (first attempt)
    @hamzake
    hamzake authored Oct 29, 2020
    Configuration menu
    Copy the full SHA
    f690c88 View commit details
    Browse the repository at this point in the history

  2. Update preprocess.py 

    Update documentation
    @hamzake
    hamzake authored Oct 29, 2020
    Configuration menu
    Copy the full SHA
    77aa88c View commit details
    Browse the repository at this point in the history

  3. Update postprocess.py 

    Add documentation
    @hamzake
    hamzake authored Oct 29, 2020
    Configuration menu
    Copy the full SHA
    c3ce457 View commit details
    Browse the repository at this point in the history

Commits on Oct 30, 2020

  1. CI: Resolved CI issues in pymialsrtk python files

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    b3c8c6b View commit details
    Browse the repository at this point in the history

  2. CI: Resolved CI issues in bidsapp py file

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    69324b9 View commit details
    Browse the repository at this point in the history

  3. Update preprocess.py 

    Add docstring to "Multiple" interfaces and to _extractBrain
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    8cb4ecc View commit details
    Browse the repository at this point in the history

  4. Update installation.rst 

    Change connectome mapper to mialsrtk
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    2f3f15d View commit details
    Browse the repository at this point in the history

  5. DOC: Update documentation of NLM denoising - multiple and single.

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    2e0a8d0 View commit details
    Browse the repository at this point in the history

  6. Merged conflicts dev-pgd-hk

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    113fc84 View commit details
    Browse the repository at this point in the history

  7. DOC: Update documentation for SliceIntensityCorrection - multiple and… 

    … single.
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    008423f View commit details
    Browse the repository at this point in the history

  8. DOC: Update documentation for SliceBySliceN4BiasFieldCorrection - mul… 

    …tiple and single.
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    0f91f7f View commit details
    Browse the repository at this point in the history

  9. Update srr.py 

    DOC: update docstrings
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    6122588 View commit details
    Browse the repository at this point in the history

  10. DOC: Update documentation for SliceBySliceCorrectBiasField - multiple… 

    … and single.
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    a0b4495 View commit details
    Browse the repository at this point in the history

  11. DOC: reviewed sphinx conf.py to browse docstrings

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    d70edd2 View commit details
    Browse the repository at this point in the history

  12. DOC: add files and update TOC of index with API documentation from do… 

    …cstrings
    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    0bfb7f1 View commit details
    Browse the repository at this point in the history

  13. Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Labora… 

    …tory/mialsuperresolutiontoolkit into dev-pgd-hk
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    23563af View commit details
    Browse the repository at this point in the history

  14. Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Labora… 

    …tory/mialsuperresolutiontoolkit into dev-pgd-hk
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    b0c16b7 View commit details
    Browse the repository at this point in the history

  15. DOC: Update documentation for MialsrtkIntensityStandardization, Mials… 

    …rtkHistogramNormalization and MialsrtkMaskImage.
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    7ad284b View commit details
    Browse the repository at this point in the history

  16. DOC: try to ignore missing modules to build doc from docstrings

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    ee45cda View commit details
    Browse the repository at this point in the history

  17. Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Labora… 

    …tory/mialsuperresolutiontoolkit into dev-pgd-hk
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    04f0d13 View commit details
    Browse the repository at this point in the history

  18. DOC: add skimage module to be ignore by readthedocs

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    2567fac View commit details
    Browse the repository at this point in the history

  19. DOC: Update on InputSpec and OutputSpec descriptions

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    95ac456 View commit details
    Browse the repository at this point in the history

  20. CI: Resolved issue on empty dictionaries

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    61a7fda View commit details
    Browse the repository at this point in the history

  21. Update preprocess.py 

    Delete global_max normalization
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    a4be1ef View commit details
    Browse the repository at this point in the history

  22. Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Labora… 

    …tory/mialsuperresolutiontoolkit into dev-pgd-hk
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    7001fa7 View commit details
    Browse the repository at this point in the history

  23. Update brainExtractionTwoSteps.py 

    Delete global_max normalization
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    e6433c6 View commit details
    Browse the repository at this point in the history

  24. Merge branch 'dev-pgd-hk' of github.com:Medical-Image-Analysis-Labora… 

    …tory/mialsuperresolutiontoolkit into dev-pgd-hk
    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    0a0da2f View commit details
    Browse the repository at this point in the history

  25. DOC: Update documentation of anatomical srr pipeline.

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    b77d22c View commit details
    Browse the repository at this point in the history

  26. DOC: Correct Postprocess page title

    @pdedumast
    pdedumast committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    7bff376 View commit details
    Browse the repository at this point in the history

  27. DOC: add contributing page with description how to build the bidsapp … 

    …and the doc locally
    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    186e73a View commit details
    Browse the repository at this point in the history

  28. MAINT: fix code style issue in script reported by codacy

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    89a3a7f View commit details
    Browse the repository at this point in the history

  29. MAINT: fix code style issue in script reported by codacy

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    e6e5ee4 View commit details
    Browse the repository at this point in the history

  30. Update preprocess.py 

    DOC: Add detailed docstring for brain extraction
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    343bb56 View commit details
    Browse the repository at this point in the history

  31. Update preprocess.py 

    DOC: add empty line between params description for brainExtraction module
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    b24e1be View commit details
    Browse the repository at this point in the history

  32. FIX: remove typo in code line 199 that made tests in circleci failing

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    d6edf0a View commit details
    Browse the repository at this point in the history

  33. Merge remote-tracking branch 'origin/dev-pgd-hk' into dev-pgd-hk

    @sebastientourbier
    sebastientourbier committed Oct 30, 2020
    Configuration menu
    Copy the full SHA
    9707aa1 View commit details
    Browse the repository at this point in the history

  34. Update preprocess.py 

    DOC: describe stacksOrder attribute
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    d973fa6 View commit details
    Browse the repository at this point in the history

  35. Update preprocess.py 

    Code changes to satisfy codacy (white spaces, variable name, overindentation, etc.)
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    e1456c1 View commit details
    Browse the repository at this point in the history

  36. Update preprocess.py 

    Code changes to satisfy codacy (white spaces, variable name, overindentation, etc.)
    @hamzake
    hamzake authored Oct 30, 2020
    Configuration menu
    Copy the full SHA
    08e224e View commit details
    Browse the repository at this point in the history

Commits on Nov 2, 2020

  1. Update srr.py 

    Change "stacksOrder" by stacks_order to adapt to change of variable in preprocess.py (to satisfy codacy)
    @hamzake
    hamzake authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    3d8714a View commit details
    Browse the repository at this point in the history

  2. Update preprocess.py 

    DOC: Include doc for InputSpec and OutputSpec and move parameters from BaseInterface to InputSpec
    @hamzake
    hamzake authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    8df484c View commit details
    Browse the repository at this point in the history

  3. Update reconstruction.py 

    Change name variable from stacksOrder to stacks_order to be compliant to preprocess.py and srr.py
    @hamzake
    hamzake authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    2a0a313 View commit details
    Browse the repository at this point in the history

  4. Update postprocess.py 

    Change variable name stacksOrder to stacks_order to be compliant to other files (preprocess, reconstruction and srr)
    @hamzake
    hamzake authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    0f96db5 View commit details
    Browse the repository at this point in the history

  5. DOC: add napoleon extension to sphinx config

    @sebastientourbier
    sebastientourbier authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    973f0a2 View commit details
    Browse the repository at this point in the history

  6. DOC: Update .readthedocs.yml to V2

    @sebastientourbier
    sebastientourbier authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    37816e1 View commit details
    Browse the repository at this point in the history

  7. Update .readthedocs.yml

    @sebastientourbier
    sebastientourbier authored Nov 2, 2020
    Configuration menu
    Copy the full SHA
    1abffeb View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2020

  1. DOC: Update postprocess.py for MialsrtkRefineHRMaskByIntersection mod… 

    …ules.
    @pdedumast
    pdedumast committed Nov 3, 2020
    Configuration menu
    Copy the full SHA
    fbdc612 View commit details
    Browse the repository at this point in the history

  2. DOC: Update postprocess.py for MialsrtkN4BiasFieldCorrection modules.

    @pdedumast
    pdedumast committed Nov 3, 2020
    Configuration menu
    Copy the full SHA
    7434c02 View commit details
    Browse the repository at this point in the history

  3. CI: Resolved white spaces issues in post-/pre- process files.

    @pdedumast
    pdedumast committed Nov 3, 2020
    Configuration menu
    Copy the full SHA
    6b0065f View commit details
    Browse the repository at this point in the history

  4. DOC: Update reconstruction.py for MialsrtkTVSuperResolution modules.

    @pdedumast
    pdedumast committed Nov 3, 2020
    Configuration menu
    Copy the full SHA
    4cb5528 View commit details
    Browse the repository at this point in the history

  5. DOC: Update reconstruction.py for ImageReconstruction module

    @pdedumast
    pdedumast committed Nov 3, 2020
    Configuration menu
    Copy the full SHA
    4598dea View commit details
    Browse the repository at this point in the history

  6. FIX: Update output_SRmask -> output_srmask which caused circleci test… 

    … to fail
    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    096ebf1 View commit details
    Browse the repository at this point in the history

  7. DOC: Add autodoc summary package to requirements.txt

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    3a51ebc View commit details
    Browse the repository at this point in the history

  8. DOC: add summary to all autodoc directives in conf.py

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    ee123a4 View commit details
    Browse the repository at this point in the history

  9. Update .readthedocs.yml

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    5568c6e View commit details
    Browse the repository at this point in the history

  10. DOC: commented autodoc_default_options in conf.py

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    77272f2 View commit details
    Browse the repository at this point in the history

  11. DOC: try autosummary in preprocess module

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    409b710 View commit details
    Browse the repository at this point in the history

  12. Update api_preprocess.rst

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    c85fa23 View commit details
    Browse the repository at this point in the history

  13. Update requirements.txt

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    f4306d1 View commit details
    Browse the repository at this point in the history

  14. Update conf.py

    @sebastientourbier
    sebastientourbier authored Nov 3, 2020
    Configuration menu
    Copy the full SHA
    a48c5ec View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2020

  1. DOC: correct docstring code style issues

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    d9cbae7 View commit details
    Browse the repository at this point in the history

  2. DOC: reviewed docstring of anatomical pipeline

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    3ced881 View commit details
    Browse the repository at this point in the history

  3. DOC: reviewed example for anatomical pipeline

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    c773500 View commit details
    Browse the repository at this point in the history

  4. DOC: update citing.rst

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    f3136a9 View commit details
    Browse the repository at this point in the history

  5. DOC: update contributing.rst

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    8108a0f View commit details
    Browse the repository at this point in the history

  6. DOC: update ABOUT the index.rst and remove link to notebook in TOC

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    b523756 View commit details
    Browse the repository at this point in the history

  7. DOC: removed section title in api_pipelines.rst

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    e515bff View commit details
    Browse the repository at this point in the history

  8. DOC: update docstrings

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    3a15e99 View commit details
    Browse the repository at this point in the history

  9. DOC: add docstrings in utils.py

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    18bf8f9 View commit details
    Browse the repository at this point in the history

  10. DOC: updated logo PNG for mialsrtk (and added SVG) where I removed C++

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    bbb8b26 View commit details
    Browse the repository at this point in the history

  11. DOC: update copyright

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    856a9de View commit details
    Browse the repository at this point in the history

  12. DOC: fix default value of input argument cwd of the run() function

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    0356c7e View commit details
    Browse the repository at this point in the history

  13. DOC: update example of run() function

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    9705c17 View commit details
    Browse the repository at this point in the history

  14. MAINT: update year in copyrights

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    6303781 View commit details
    Browse the repository at this point in the history

  15. MAINT: removed unnecessary self as input of the run() function

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    ca392b0 View commit details
    Browse the repository at this point in the history

  16. MAINT: fix a number of codacy code style issues

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    33fdb2f View commit details
    Browse the repository at this point in the history

  17. DOC: add missing docstrings

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    b996b57 View commit details
    Browse the repository at this point in the history

  18. MAINT: reviewed structure of outputs for multiple reconstruction of t… 

    …he same subject
    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    14c5c83 View commit details
    Browse the repository at this point in the history

  19. MAINT: fix code style issues in setup.py

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    78e2811 View commit details
    Browse the repository at this point in the history

  20. MAINT: fix additional code style issues reported by codacy

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    db35eb4 View commit details
    Browse the repository at this point in the history

  21. CI: comment comparison with list of outputs before update

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    677279a View commit details
    Browse the repository at this point in the history

  22. MAINT: Correct code style issues in dockerfile

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    1da789c View commit details
    Browse the repository at this point in the history

  23. MAINT: fix code style and add docstrings

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    3674edd View commit details
    Browse the repository at this point in the history

  24. DOC: add docstring to get_parser()

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    8971a3b View commit details
    Browse the repository at this point in the history

  25. MAINT: fix code style issues

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    09cd838 View commit details
    Browse the repository at this point in the history

  26. MAINT: shorten long line in srr.py

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    5714f97 View commit details
    Browse the repository at this point in the history

  27. MAINT: fixed indentation

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    fd16d70 View commit details
    Browse the repository at this point in the history

  28. MAINT: remove unnecessary comments

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    771a1c4 View commit details
    Browse the repository at this point in the history

  29. MAINT: fix double quote issue in build_sphinx_docs.sh

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    9ea7143 View commit details
    Browse the repository at this point in the history

  30. MAINT: should fix issues in README

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    3e2eb19 View commit details
    Browse the repository at this point in the history

  31. DOC: add missing label for reference of contributing page

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    3e33fd4 View commit details
    Browse the repository at this point in the history

  32. DOC: add generation of PDF to .readthedocs.yml config

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    241af0f View commit details
    Browse the repository at this point in the history

  33. DOC: add link to all contributors specification in contributing.rst [… 

    …skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    ed3d75d View commit details
    Browse the repository at this point in the history

  34. DOC: updated README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    8b6ccfa View commit details
    Browse the repository at this point in the history

  35. DOC: update list of resources in README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    4764f7c View commit details
    Browse the repository at this point in the history

  36. DOC: update README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    421f0f9 View commit details
    Browse the repository at this point in the history

  37. FIX: changed log_directory in srr.py

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    048d215 View commit details
    Browse the repository at this point in the history

  38. MAINT: correct code style issue in README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    95ffeea View commit details
    Browse the repository at this point in the history

  39. MAINT: correct code style issue in README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    7b9f644 View commit details
    Browse the repository at this point in the history

  40. MAINT: correct code style issue in README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    362872a View commit details
    Browse the repository at this point in the history

  41. DOC: add page for contributors [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    20ba446 View commit details
    Browse the repository at this point in the history

  42. DOC: removed versions of required python packages

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    65e4701 View commit details
    Browse the repository at this point in the history

  43. DOC: reviewed layout in contributors as it is not properly built [ski… 

    …p ci]
    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    41775d4 View commit details
    Browse the repository at this point in the history

  44. DOC: add extra blank line at end of contributors.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    30ccd27 View commit details
    Browse the repository at this point in the history

  45. DOC: renamed hamzake -> Hamza Kebiri in contributors.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    5f101ee View commit details
    Browse the repository at this point in the history

  46. DOC: reviewed order in TOC of index.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    ba5f9aa View commit details
    Browse the repository at this point in the history

  47. CI: reduce number of stacks in data/code/participants_params.json [sk… 

    …ip ci]
    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    aef9b6b View commit details
    Browse the repository at this point in the history

  48. CI: updated list of outputs and uncommented difference checks

    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    dcfdc48 View commit details
    Browse the repository at this point in the history

  49. DOC: update outputs with new structure and add execution workflow PNG… 

    … image
    @sebastientourbier
    sebastientourbier committed Nov 4, 2020
    Configuration menu
    Copy the full SHA
    af00c0e View commit details
    Browse the repository at this point in the history

Commits on Nov 5, 2020

  1. CI: comment check diff of test-02 outputs

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    c74e31d View commit details
    Browse the repository at this point in the history

  2. CI: update output list of test-01

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    125aa92 View commit details
    Browse the repository at this point in the history

  3. DOC: update outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    5c73f26 View commit details
    Browse the repository at this point in the history

  4. DOC: rearranged bids entities description and table in outputs.rst [s… 

    …kip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    b15dc08 View commit details
    Browse the repository at this point in the history

  5. DOC: fix bids entities table in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    06609b5 View commit details
    Browse the repository at this point in the history

  6. DOC: update intro with BIDS in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    ccb46aa View commit details
    Browse the repository at this point in the history

  7. CI: update test-02 output list and re-enable to check difference

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    75881aa View commit details
    Browse the repository at this point in the history

  8. DOC: fix bids entities table in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    5de9b06 View commit details
    Browse the repository at this point in the history

  9. DOC: fix bids entities table in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    95d0191 View commit details
    Browse the repository at this point in the history

  10. DOC: reviewed labels for generalization in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    ac55522 View commit details
    Browse the repository at this point in the history

  11. DOC: resized logo in index.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    4304257 View commit details
    Browse the repository at this point in the history

  12. DOC: resized logo in index.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    e774e3e View commit details
    Browse the repository at this point in the history

  13. DOC: resized images in outputs.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    72e50d0 View commit details
    Browse the repository at this point in the history

  14. DOC: make the line below headers bigger in table of outputs.rst [skip… 

    … ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    367fe54 View commit details
    Browse the repository at this point in the history

  15. DOC: reviewed level of markers for section/subsection title in index.… 

    …rst [skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    87eef77 View commit details
    Browse the repository at this point in the history

  16. DOC: reviewed latex settings for PDF generation in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    25a4352 View commit details
    Browse the repository at this point in the history

  17. DOC: reviewed level of markers for section/subsection title in index.… 

    …rst [skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    66465dc View commit details
    Browse the repository at this point in the history

  18. DOC: add info to add contributor to the list in the README [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    1e55459 View commit details
    Browse the repository at this point in the history

  19. DEL: Remove empty scripts/superresolution script and folder [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    99372f7 View commit details
    Browse the repository at this point in the history

  20. DOC: update info to add contributor to the list [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    aafe470 View commit details
    Browse the repository at this point in the history

  21. DOC: update info to add contributor to the list [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    32e46bd View commit details
    Browse the repository at this point in the history

  22. DOC: update info to add contributor to the list [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    a0b7514 View commit details
    Browse the repository at this point in the history

  23. DOC: shorten title to Contributing in contributing.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    1a8b6b2 View commit details
    Browse the repository at this point in the history

  24. DOC: Add missing contribution type section title in contributing.rst … 

    …[skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    86085eb View commit details
    Browse the repository at this point in the history

  25. DOC: renamed title to Pipelines module in api_pipelines.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    32e934f View commit details
    Browse the repository at this point in the history

  26. DOC: move one level up section "not list as contributor?" in contribu… 

    …ting.rst [skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    e73bcab View commit details
    Browse the repository at this point in the history

  27. DOC: fix typo in contributing.rst [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    72d80ba View commit details
    Browse the repository at this point in the history

  28. DOC: reviewed about in README and index.rst and modified text highlig… 

    …ht [skip ci]
    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    dedb53e View commit details
    Browse the repository at this point in the history

  29. DOC: reviewed more text highlights [skip ci]

    @sebastientourbier
    sebastientourbier committed Nov 5, 2020
    Configuration menu
    Copy the full SHA
    d0b7de2 View commit details
    Browse the repository at this point in the history

Commits on Nov 6, 2020

  1. DOC: update readthedocs conf.py for better PDF generation [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    874d856 View commit details
    Browse the repository at this point in the history

  2. DOC: comment latex_engine definition in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    5e22e1b View commit details
    Browse the repository at this point in the history

  3. DOC: update customization latex and removed to show version in conf.p… 

    …y [skip ci]
    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    798b6d4 View commit details
    Browse the repository at this point in the history

  4. DOC: adjust code size and improve comments for latex in conf.py [skip… 

    … ci]
    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    588ca2f View commit details
    Browse the repository at this point in the history

  5. DOC: fix latex_elements in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    ef1c7e1 View commit details
    Browse the repository at this point in the history

  6. DOC: install fontspec for latex in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    d6ab04f View commit details
    Browse the repository at this point in the history

  7. DOC: install fontspec for latex in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    c0577a4 View commit details
    Browse the repository at this point in the history

  8. DOC: try to fix customization of font family for latex in conf.py [sk… 

    …ip ci]
    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    6d5cc09 View commit details
    Browse the repository at this point in the history

  9. DOC: install dejavu font for PDF in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    3e3ef25 View commit details
    Browse the repository at this point in the history

  10. DOC: an other try to fix column of index for pdf in conf.py [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    8727491 View commit details
    Browse the repository at this point in the history

  11. DOC: reuse fvset to adjust code but seems to still not working [skip ci]

    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    f2d2333 View commit details
    Browse the repository at this point in the history

  12. DOC: disable custom fvset and makeindex as they do not work properly … 

    …[skip ci]
    @sebastientourbier
    sebastientourbier authored Nov 6, 2020
    Configuration menu
    Copy the full SHA
    31ef25a View commit details
    Browse the repository at this point in the history