shimming-toolbox / shimming-toolbox / 10404856405

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first iteration to adding BET (#542)

* first iteration to adding BET

* Change output file

* better code

* add erode/dilate

* modifs

* add json file in erode/dilate

* Update fsleyes-plugin-shimming-toolbox/fsleyes_plugin_shimming_toolbox/tabs/mask_tab.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimming-toolbox/shimmingtoolbox/cli/mask.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* fix error

* fix naming issues + add tests for BET and erode/dilate tab

* Add fsl download

* test

* test

* Test macos

* add tests for each mask option

* test download bet using conda

* change bet to bet2

* fix default output name for bet

* review comments

* change bet for bet2

* small modifs

* correction

* Update .github/workflows/tests.yml

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update fsleyes-plugin-shimming-toolbox/test/gui/test_mask_tab.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimming-toolbox/shimmingtoolbox/cli/mask.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update fsleyes-plugin-shimming-toolbox/fsleyes_plugin_shimming_toolbox/tabs/mask_tab.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* review comments

* check if bet is installed in st_check_dependecies

* add pytest.ini to fsleyes-plugin

* add version check for bet

* fix issue

* fix test

* fix ber marker for fsleyes-plugin

* Update shimming-toolbox/shimmingtoolbox/cli/check_env.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Update shimming-toolbox/shimmingtoolbox/cli/check_env.py

Co-authored-by: Alex Dastous <47249340+po09i@users.noreply.github.com>

* Print Bet version in st_check_dependencies

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Co-authored-by: Alex Dastous <47249340+po09i@users.no... (continued)

36 of 78 new or added lines in 2 files covered. (46.15%)

4972 of 5448 relevant lines covered (91.26%)

3.65 hits per line