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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

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3b904ad
first iteration of the defacing LORIS script
cmadjar Dec 5, 2018
cc92143
pipeline works fully and register defaced images in LORIS for simple …
cmadjar Dec 6, 2018
7042404
perldoc of the functions
cmadjar Dec 6, 2018
17020e0
check that the files of the session were not already defaced
cmadjar Dec 6, 2018
354eaea
updated queries for fileIDs so that it queries only the right file fo…
cmadjar Dec 6, 2018
f225453
added documentation for function check_if_deface_files_already_in_db
cmadjar Dec 7, 2018
afca912
added latest development version of deface_minipipe.pl
cmadjar Dec 14, 2018
86680ab
finished tool script to deface and register defaced images in LORIS
cmadjar Dec 14, 2018
c23a93d
fixed use of unitialized value in File.pm and MRI.pm when running the…
cmadjar Dec 14, 2018
0463e0f
updated comments on top of constant variables of the tool script
cmadjar Jan 4, 2019
6353243
Nicolas' feedback on deface_minipipe.pl
cmadjar Jan 4, 2019
3943c40
Nicolas' feedback
cmadjar Jan 10, 2019
4b83fb6
Mélanie's comment and added the MD file for the new tool in the docs/…
cmadjar Jan 14, 2019
61295ee
Melanie's feedback
cmadjar Jan 15, 2019
4b28b43
modified deface_minipipe.pl so that by default it uses the t1 model
cmadjar Feb 6, 2019
70fef00
added the mni models and beast library to the README in the requireme…
cmadjar Feb 6, 2019
bbec09f
Removed version from the bic-mni-models and beast-library packages in…
cmadjar Feb 11, 2019
838c04b
great catch from Nicolas :)
cmadjar Feb 19, 2019
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Expand Up @@ -12,3 +12,6 @@ source /data/%PROJECT%/bin/mri/python_virtualenvs/loris-mri-python/bin/activate
source %MINC_TOOLKIT_DIR%/minc-toolkit-config.sh
umask 0002

# for the defacing scripts
export BEASTLIB=%MINC_TOOLKIT_DIR%/../share/beast-library-1.1
export MNI_MODELS=%MINC_TOOLKIT_DIR%/../share/icbm152_model_09c
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