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

Addition of a LORIS tool to deface structural images and register the defaced images back into LORIS #366

Merged
merged 18 commits into from
Feb 19, 2019
Merged

Addition of a LORIS tool to deface structural images and register the defaced images back into LORIS #366

merged 18 commits into from
Feb 19, 2019

Commits on Dec 5, 2018

  1. first iteration of the defacing LORIS script

    @cmadjar
    cmadjar committed Dec 5, 2018
    Configuration menu
    Copy the full SHA
    3b904ad View commit details
    Browse the repository at this point in the history

Commits on Dec 6, 2018

  1. pipeline works fully and register defaced images in LORIS for simple … 

    …acquisitions like t1, t2, flair etc... Need to work on multi-echo acquisitions and MP2RAGE now
    @cmadjar
    cmadjar committed Dec 6, 2018
    Configuration menu
    Copy the full SHA
    cc92143 View commit details
    Browse the repository at this point in the history

  2. perldoc of the functions

    @cmadjar
    cmadjar committed Dec 6, 2018
    Configuration menu
    Copy the full SHA
    7042404 View commit details
    Browse the repository at this point in the history

  3. check that the files of the session were not already defaced

    @cmadjar
    cmadjar committed Dec 6, 2018
    Configuration menu
    Copy the full SHA
    17020e0 View commit details
    Browse the repository at this point in the history

  4. updated queries for fileIDs so that it queries only the right file fo… 

    …r special acquisition types such as MP2RAGE base on the minc header acquisition:image_type
    @cmadjar
    cmadjar committed Dec 6, 2018
    Configuration menu
    Copy the full SHA
    354eaea View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2018

  1. added documentation for function check_if_deface_files_already_in_db

    @cmadjar
    cmadjar committed Dec 7, 2018
    Configuration menu
    Copy the full SHA
    f225453 View commit details
    Browse the repository at this point in the history

Commits on Dec 14, 2018

  1. added latest development version of deface_minipipe.pl

    @cmadjar
    cmadjar committed Dec 14, 2018
    Configuration menu
    Copy the full SHA
    afca912 View commit details
    Browse the repository at this point in the history

  2. finished tool script to deface and register defaced images in LORIS

    @cmadjar
    cmadjar committed Dec 14, 2018
    Configuration menu
    Copy the full SHA
    86680ab View commit details
    Browse the repository at this point in the history

  3. fixed use of unitialized value in File.pm and MRI.pm when running the… 

    … script
    @cmadjar
    cmadjar committed Dec 14, 2018
    Configuration menu
    Copy the full SHA
    c23a93d View commit details
    Browse the repository at this point in the history

Commits on Jan 4, 2019

  1. updated comments on top of constant variables of the tool script

    @cmadjar
    cmadjar committed Jan 4, 2019
    Configuration menu
    Copy the full SHA
    0463e0f View commit details
    Browse the repository at this point in the history

  2. Nicolas' feedback on deface_minipipe.pl

    @cmadjar
    cmadjar committed Jan 4, 2019
    Configuration menu
    Copy the full SHA
    6353243 View commit details
    Browse the repository at this point in the history

Commits on Jan 10, 2019

  1. Nicolas' feedback

    @cmadjar
    cmadjar committed Jan 10, 2019
    Configuration menu
    Copy the full SHA
    3943c40 View commit details
    Browse the repository at this point in the history

Commits on Jan 14, 2019

  1. Mélanie's comment and added the MD file for the new tool in the docs/… 

    …scripts_md directory
    @cmadjar
    cmadjar committed Jan 14, 2019
    Configuration menu
    Copy the full SHA
    4b83fb6 View commit details
    Browse the repository at this point in the history

Commits on Jan 15, 2019

  1. Melanie's feedback

    @cmadjar
    cmadjar committed Jan 15, 2019
    Configuration menu
    Copy the full SHA
    61295ee View commit details
    Browse the repository at this point in the history

Commits on Feb 6, 2019

  1. modified deface_minipipe.pl so that by default it uses the t1 model

    @cmadjar
    cmadjar committed Feb 6, 2019
    Configuration menu
    Copy the full SHA
    4b28b43 View commit details
    Browse the repository at this point in the history

  2. added the mni models and beast library to the README in the requireme… 

    …nts for defacing scripts
    @cmadjar
    cmadjar committed Feb 6, 2019
    Configuration menu
    Copy the full SHA
    70fef00 View commit details
    Browse the repository at this point in the history

Commits on Feb 11, 2019

  1. Removed version from the bic-mni-models and beast-library packages in… 

    … the README.md
    @cmadjar
    cmadjar committed Feb 11, 2019
    Configuration menu
    Copy the full SHA
    bbec09f View commit details
    Browse the repository at this point in the history

Commits on Feb 19, 2019

  1. great catch from Nicolas :)

    @cmadjar
    cmadjar committed Feb 19, 2019
    Configuration menu
    Copy the full SHA
    838c04b View commit details
    Browse the repository at this point in the history