Refactored WM atlas creation pipeline and improved documentation #1492
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
jcohenadad
added
enhancement
…olbox into jca_refactorAtlas * 'jca_refactorAtlas' of github.com:neuropoly/spinalcordtoolbox: Added key bindings to the undo, save and help actions. (#1480)
stephaniealley
approved these changes
Oct 13, 2017
jcohenadad
added a commit
that referenced
this pull request
Oct 27, 2017
* master: (43 commits) BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md download_data: forgot to add pmj_models in the -d flag ...
jcohenadad
added a commit
that referenced
this pull request
Oct 27, 2017
* jca-release: (44 commits) updated CHANGES for 3.1 BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md ... # Conflicts: # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py
jcohenadad
added a commit
that referenced
this pull request
Dec 18, 2019
* jca-release: (44 commits) updated CHANGES for 3.1 BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md ... # Conflicts: # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py Former-commit-id: 45518c6
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The main modification is that the file
create_atlas.mis now a function (previously a script) that calls a parameter.m file, which is set for each project