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Title: Commits · allaaamr/preprocessing · GitHub

Open Graph Title: Commits · allaaamr/preprocessing

X Title: Commits · allaaamr/preprocessing

Description: preprocessing tools for multi-modal 3D brain MRI. Contribute to allaaamr/preprocessing development by creating an account on GitHub.

Open Graph Description: preprocessing tools for multi-modal 3D brain MRI. Contribute to allaaamr/preprocessing development by creating an account on GitHub.

X Description: preprocessing tools for multi-modal 3D brain MRI. Contribute to allaaamr/preprocessing development by creating an account on GitHub.

Opengraph URL: https://github.com/allaaamr/preprocessing

X: @github

direct link

Domain: github.com

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Skip to content	https://github.com/allaaamr/preprocessing/commits#start-of-content
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Reload	https://github.com/allaaamr/preprocessing/commits
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allaaamr	https://github.com/allaaamr
preprocessing	https://github.com/allaaamr/preprocessing
BrainLesion/preprocessing	https://github.com/BrainLesion/preprocessing
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Merge branch 'main' of https://github.com/allaaamr/preprocessing	https://github.com/allaaamr/preprocessing/commit/09bd48cef1c657162defea030e369bd1027213d4
	https://github.com/allaaamr
allaaamr	https://github.com/allaaamr/preprocessing/commits?author=allaaamr
09bd48c	https://github.com/allaaamr/preprocessing/commit/09bd48cef1c657162defea030e369bd1027213d4
	https://github.com/allaaamr/preprocessing/tree/09bd48cef1c657162defea030e369bd1027213d4
TCGA-02-0003	https://github.com/allaaamr/preprocessing/commit/9f2e5e60a0af4506321139504257ba97ca7298b4
	https://github.com/allaaamr
allaaamr	https://github.com/allaaamr/preprocessing/commits?author=allaaamr
9f2e5e6	https://github.com/allaaamr/preprocessing/commit/9f2e5e60a0af4506321139504257ba97ca7298b4
	https://github.com/allaaamr/preprocessing/tree/9f2e5e60a0af4506321139504257ba97ca7298b4
sample	https://github.com/allaaamr/preprocessing/commit/990fff3911dc954b74368c15a3094fcaee9858d5
990fff3	https://github.com/allaaamr/preprocessing/commit/990fff3911dc954b74368c15a3094fcaee9858d5
	https://github.com/allaaamr/preprocessing/tree/990fff3911dc954b74368c15a3094fcaee9858d5
script for running pipiline on server	https://github.com/allaaamr/preprocessing/commit/6bc43f04e784a27ea95e42fe8a0fca407c3d5797
	https://github.com/allaaamr
allaaamr	https://github.com/allaaamr/preprocessing/commits?author=allaaamr
6bc43f0	https://github.com/allaaamr/preprocessing/commit/6bc43f04e784a27ea95e42fe8a0fca407c3d5797
	https://github.com/allaaamr/preprocessing/tree/6bc43f04e784a27ea95e42fe8a0fca407c3d5797
Merge pull request #102 from BrainLesion/101-standardized-issue-templates	https://github.com/allaaamr/preprocessing/commit/eea756550d9758664182c5f1980b2993ccd4edf7
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
eea7565	https://github.com/allaaamr/preprocessing/commit/eea756550d9758664182c5f1980b2993ccd4edf7
	https://github.com/allaaamr/preprocessing/tree/eea756550d9758664182c5f1980b2993ccd4edf7
hui	https://github.com/allaaamr/preprocessing/commit/8a7280af57f81bef6b67c35963bc53bc25a0d3f3
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
8a7280a	https://github.com/allaaamr/preprocessing/commit/8a7280af57f81bef6b67c35963bc53bc25a0d3f3
	https://github.com/allaaamr/preprocessing/tree/8a7280af57f81bef6b67c35963bc53bc25a0d3f3
Merge pull request #98 from BrainLesion/97-defacing-is-missing-in-the-docs	https://github.com/allaaamr/preprocessing/commit/a863b9cc11b36dc7a7c8f4ee300e1323f7489907
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
a863b9c	https://github.com/allaaamr/preprocessing/commit/a863b9cc11b36dc7a7c8f4ee300e1323f7489907
	https://github.com/allaaamr/preprocessing/tree/a863b9cc11b36dc7a7c8f4ee300e1323f7489907
Add defacing outputs to example	https://github.com/allaaamr/preprocessing/commit/7c8816eace05bf467812226ef78bce2f25de3373
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
7c8816e	https://github.com/allaaamr/preprocessing/commit/7c8816eace05bf467812226ef78bce2f25de3373
	https://github.com/allaaamr/preprocessing/tree/7c8816eace05bf467812226ef78bce2f25de3373
Add defacing to docs	https://github.com/allaaamr/preprocessing/commit/6d540633a6af7159f09297e60af0b255280b847f
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
6d54063	https://github.com/allaaamr/preprocessing/commit/6d540633a6af7159f09297e60af0b255280b847f
	https://github.com/allaaamr/preprocessing/tree/6d540633a6af7159f09297e60af0b255280b847f
Merge pull request #96 from BrainLesion/91-remove-example-data	https://github.com/allaaamr/preprocessing/commit/af0206e7eb3d3e3fc7dc3f7b48647add5812fdb5
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
af0206e	https://github.com/allaaamr/preprocessing/commit/af0206e7eb3d3e3fc7dc3f7b48647add5812fdb5
	https://github.com/allaaamr/preprocessing/tree/af0206e7eb3d3e3fc7dc3f7b48647add5812fdb5
we no longer have output files in the repo, as these are always changing with our ongoing development	https://github.com/allaaamr/preprocessing/commit/1c4251cfc0e43beabef421cc02135962bda4dd03
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
1c4251c	https://github.com/allaaamr/preprocessing/commit/1c4251cfc0e43beabef421cc02135962bda4dd03
	https://github.com/allaaamr/preprocessing/tree/1c4251cfc0e43beabef421cc02135962bda4dd03
Merge pull request #95 from BrainLesion/94-ants-is-our-default-registrator-but-not-installed-by-default	https://github.com/allaaamr/preprocessing/commit/7754299d86f4c818d79771efa585d1e493c9fb7c
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
7754299	https://github.com/allaaamr/preprocessing/commit/7754299d86f4c818d79771efa585d1e493c9fb7c
	https://github.com/allaaamr/preprocessing/tree/7754299d86f4c818d79771efa585d1e493c9fb7c
Read warning	https://github.com/allaaamr/preprocessing/commit/00e94c97b7eafcd594ee5bd2c1497c2a0516d5a9
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
00e94c9	https://github.com/allaaamr/preprocessing/commit/00e94c97b7eafcd594ee5bd2c1497c2a0516d5a9
	https://github.com/allaaamr/preprocessing/tree/00e94c97b7eafcd594ee5bd2c1497c2a0516d5a9
Remove irrelevant warning	https://github.com/allaaamr/preprocessing/commit/7ecb01803c22dd6026f9dbac8abe6db48f36f4f9
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
7ecb018	https://github.com/allaaamr/preprocessing/commit/7ecb01803c22dd6026f9dbac8abe6db48f36f4f9
	https://github.com/allaaamr/preprocessing/tree/7ecb01803c22dd6026f9dbac8abe6db48f36f4f9
Install antspyx by default	https://github.com/allaaamr/preprocessing/commit/0d811ccfa4835e64906a479bd655fc78c99dc564
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
0d811cc	https://github.com/allaaamr/preprocessing/commit/0d811ccfa4835e64906a479bd655fc78c99dc564
	https://github.com/allaaamr/preprocessing/tree/0d811ccfa4835e64906a479bd655fc78c99dc564
Merge pull request #93 from BrainLesion/88-feature-request-allow-user-to-save-bet-and-defacing-masks	https://github.com/allaaamr/preprocessing/commit/f8a395b0671b851d8d7206871bec6f3b59152c98
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
f8a395b	https://github.com/allaaamr/preprocessing/commit/f8a395b0671b851d8d7206871bec6f3b59152c98
	https://github.com/allaaamr/preprocessing/tree/f8a395b0671b851d8d7206871bec6f3b59152c98
Update README.md	https://github.com/allaaamr/preprocessing/commit/233857c687db3700f103df880d9b4f7a622683e8
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
233857c	https://github.com/allaaamr/preprocessing/commit/233857c687db3700f103df880d9b4f7a622683e8
	https://github.com/allaaamr/preprocessing/tree/233857c687db3700f103df880d9b4f7a622683e8
Fix inconsistent naming	https://github.com/allaaamr/preprocessing/commit/ddf7ad314dee58fdad656df6ff3efebf25b0733c
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
ddf7ad3	https://github.com/allaaamr/preprocessing/commit/ddf7ad314dee58fdad656df6ff3efebf25b0733c
	https://github.com/allaaamr/preprocessing/tree/ddf7ad314dee58fdad656df6ff3efebf25b0733c
Update README.md	https://github.com/allaaamr/preprocessing/commit/bf4af58a237675291fe0f64e0aba0a2a29c1b28f
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
bf4af58	https://github.com/allaaamr/preprocessing/commit/bf4af58a237675291fe0f64e0aba0a2a29c1b28f
	https://github.com/allaaamr/preprocessing/tree/bf4af58a237675291fe0f64e0aba0a2a29c1b28f
Add mask outputs to example	https://github.com/allaaamr/preprocessing/commit/790275be0b25b52bf7773aa29470975e837f173e
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
790275b	https://github.com/allaaamr/preprocessing/commit/790275be0b25b52bf7773aa29470975e837f173e
	https://github.com/allaaamr/preprocessing/tree/790275be0b25b52bf7773aa29470975e837f173e
Simplify imports	https://github.com/allaaamr/preprocessing/commit/921961269ce412e02f5b34c60aafdf882a69a2e2
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
9219612	https://github.com/allaaamr/preprocessing/commit/921961269ce412e02f5b34c60aafdf882a69a2e2
	https://github.com/allaaamr/preprocessing/tree/921961269ce412e02f5b34c60aafdf882a69a2e2
Add class docstrings for CenterModality	https://github.com/allaaamr/preprocessing/commit/4d27031cf6e9de96452a0beac2b95dbaa28fdf35
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
4d27031	https://github.com/allaaamr/preprocessing/commit/4d27031cf6e9de96452a0beac2b95dbaa28fdf35
	https://github.com/allaaamr/preprocessing/tree/4d27031cf6e9de96452a0beac2b95dbaa28fdf35
Update example to use CenterModality	https://github.com/allaaamr/preprocessing/commit/c4de0f523df708adf7ef88b15aef28fb0ad86301
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
c4de0f5	https://github.com/allaaamr/preprocessing/commit/c4de0f523df708adf7ef88b15aef28fb0ad86301
	https://github.com/allaaamr/preprocessing/tree/c4de0f523df708adf7ef88b15aef28fb0ad86301
Change warning to deprecation	https://github.com/allaaamr/preprocessing/commit/205dc3bae2cbc035f7e4701bd6dcb417843a0ae5
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
205dc3b	https://github.com/allaaamr/preprocessing/commit/205dc3bae2cbc035f7e4701bd6dcb417843a0ae5
	https://github.com/allaaamr/preprocessing/tree/205dc3bae2cbc035f7e4701bd6dcb417843a0ae5
Update docs and add warning to sue center modality class	https://github.com/allaaamr/preprocessing/commit/1884089d4753ce2f75d331ac1364b5aa3858b4b4
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
1884089	https://github.com/allaaamr/preprocessing/commit/1884089d4753ce2f75d331ac1364b5aa3858b4b4
	https://github.com/allaaamr/preprocessing/tree/1884089d4753ce2f75d331ac1364b5aa3858b4b4
Adding CenterModality subclass to allow elegantly saving masks	https://github.com/allaaamr/preprocessing/commit/37d3fe03badc75f53b2dfd9b6247e5a599d05f1b
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
37d3fe0	https://github.com/allaaamr/preprocessing/commit/37d3fe03badc75f53b2dfd9b6247e5a599d05f1b
	https://github.com/allaaamr/preprocessing/tree/37d3fe03badc75f53b2dfd9b6247e5a599d05f1b
Merge pull request #85 from BrainLesion/84-add-minimal-example-to-readme	https://github.com/allaaamr/preprocessing/commit/bfcfc8685296a4d4cfcd89f886698e3e866e9aaa
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
bfcfc86	https://github.com/allaaamr/preprocessing/commit/bfcfc8685296a4d4cfcd89f886698e3e866e9aaa
	https://github.com/allaaamr/preprocessing/tree/bfcfc8685296a4d4cfcd89f886698e3e866e9aaa
Update example	https://github.com/allaaamr/preprocessing/commit/f310a48f91e1b665f12a3d029fbad34dfb4a8d2f
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
f310a48	https://github.com/allaaamr/preprocessing/commit/f310a48f91e1b665f12a3d029fbad34dfb4a8d2f
	https://github.com/allaaamr/preprocessing/tree/f310a48f91e1b665f12a3d029fbad34dfb4a8d2f
Merge branch 'main' into 84-add-minimal-example-to-readme	https://github.com/allaaamr/preprocessing/commit/ced342b443cedc10ad0c373e06e7b731893e71c5
	https://github.com/MarcelRosier
MarcelRosier	https://github.com/allaaamr/preprocessing/commits?author=MarcelRosier
ced342b	https://github.com/allaaamr/preprocessing/commit/ced342b443cedc10ad0c373e06e7b731893e71c5
	https://github.com/allaaamr/preprocessing/tree/ced342b443cedc10ad0c373e06e7b731893e71c5
Merge pull request #90 from yasinzaii/main	https://github.com/allaaamr/preprocessing/commit/e6c139c69c09afbfcf630b0e57bf7798a05fa9ba
	https://github.com/neuronflow
neuronflow	https://github.com/allaaamr/preprocessing/commits?author=neuronflow
e6c139c	https://github.com/allaaamr/preprocessing/commit/e6c139c69c09afbfcf630b0e57bf7798a05fa9ba
	https://github.com/allaaamr/preprocessing/tree/e6c139c69c09afbfcf630b0e57bf7798a05fa9ba
Corrected QuickshearDefacer argument name mismatch	https://github.com/allaaamr/preprocessing/commit/a707c4e9b208d0af618dcf5d701abaf54cbdcb58
	https://github.com/yasinzaii
yasinzaii	https://github.com/allaaamr/preprocessing/commits?author=yasinzaii
a707c4e	https://github.com/allaaamr/preprocessing/commit/a707c4e9b208d0af618dcf5d701abaf54cbdcb58
	https://github.com/allaaamr/preprocessing/tree/a707c4e9b208d0af618dcf5d701abaf54cbdcb58
Moved atlas_dir definition from Preprocessor class init fun to run_atlas_registration fun.	https://github.com/allaaamr/preprocessing/commit/36be733bfd77489d3f8bc75ad058d7e342e977b8
	https://github.com/yasinzaii
yasinzaii	https://github.com/allaaamr/preprocessing/commits?author=yasinzaii
36be733	https://github.com/allaaamr/preprocessing/commit/36be733bfd77489d3f8bc75ad058d7e342e977b8
	https://github.com/allaaamr/preprocessing/tree/36be733bfd77489d3f8bc75ad058d7e342e977b8
Moved Logging Configuration out of Preprocessor.py	https://github.com/allaaamr/preprocessing/commit/d61f649b843973c5e366fdd8248efa9091a2d1b2
	https://github.com/yasinzaii
yasinzaii	https://github.com/allaaamr/preprocessing/commits?author=yasinzaii
d61f649	https://github.com/allaaamr/preprocessing/commit/d61f649b843973c5e366fdd8248efa9091a2d1b2
	https://github.com/allaaamr/preprocessing/tree/d61f649b843973c5e366fdd8248efa9091a2d1b2
Reformatted code using black to fix linting issues	https://github.com/allaaamr/preprocessing/commit/b4751feb95a8c1528b020b2eed60a9628727823b
	https://github.com/yasinzaii
yasinzaii	https://github.com/allaaamr/preprocessing/commits?author=yasinzaii
b4751fe	https://github.com/allaaamr/preprocessing/commit/b4751feb95a8c1528b020b2eed60a9628727823b
	https://github.com/allaaamr/preprocessing/tree/b4751feb95a8c1528b020b2eed60a9628727823b
Code Updates and Cleaning, Bux Fixes	https://github.com/allaaamr/preprocessing/commit/1cde873236bfd8d2846e62066cdbe1b661d40d18
yasinzaii	https://github.com/allaaamr/preprocessing/commits?author=yasinzaii
1cde873	https://github.com/allaaamr/preprocessing/commit/1cde873236bfd8d2846e62066cdbe1b661d40d18
	https://github.com/allaaamr/preprocessing/tree/1cde873236bfd8d2846e62066cdbe1b661d40d18
Next	https://github.com/allaaamr/preprocessing/commits?after=09bd48cef1c657162defea030e369bd1027213d4+34
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