Code

08MQ reproduction#121

Code

Merged

bclenet merged 129 commits intoInria-Empenn:mainInria-Empenn/narps_open_pipelines:mainfrom bclenet:08MQ_reproductionbclenet/narps_open_pipelines:08MQ_reproductionCopy head branch name to clipboardJan 4, 2024

+1,294-11

Commits

Commits on Aug 31, 2023

• [BUG] inside unit_tests workflow

  bclenet

  committed
  6986e90

  Copy full SHA for 6986e90

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  d6e67f3

  Copy full SHA for d6e67f3

Commits on Sep 4, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  c3bfc53

  Copy full SHA for c3bfc53

Commits on Sep 19, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  4b30504

  Copy full SHA for 4b30504

Commits on Sep 21, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  fd15ffc

  Copy full SHA for fd15ffc

Commits on Sep 29, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  6ebe5d2

  Copy full SHA for 6ebe5d2

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  0a584dd

  Copy full SHA for 0a584dd

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  e284b80

  Copy full SHA for e284b80

Commits on Oct 5, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  5774813

  Copy full SHA for 5774813

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  8f12d3d

  Copy full SHA for 8f12d3d

Commits on Oct 6, 2023

• [08MQ] Preprocessing script in progress

  bclenet

  committed
  7fde1e1

  Copy full SHA for 7fde1e1

Commits on Oct 9, 2023

• Working on preprocessing

  bclenet

  committed
  2b07afc

  Copy full SHA for 2b07afc

• Codespell

  bclenet

  committed
  a454652

  Copy full SHA for a454652

Commits on Oct 10, 2023

• Working on pipeline 08MQ

  bclenet

  committed
  aca4896

  Copy full SHA for aca4896

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  91dc744

  Copy full SHA for 91dc744

Commits on Oct 11, 2023

• Towards a running version of the pipeline

  bclenet

  committed
  8b48823

  Copy full SHA for 8b48823

• Conforming to Pipeline class + init test module

  bclenet

  committed
  ecec8c2

  Copy full SHA for ecec8c2

• Merge branch 'main' into 08MQ_reproduction

  bclenet

  committed
  c8db382

  Copy full SHA for c8db382

• Towards a running version of the pipeline

  bclenet

  committed
  632f4ef

  Copy full SHA for 632f4ef

• Towards a running version of the pipeline

  bclenet

  committed
  0e97a61

  Copy full SHA for 0e97a61

Commits on Oct 13, 2023

• Towards a running version of the pipeline

  bclenet

  committed
  d3dcc00

  Copy full SHA for d3dcc00

• [TEST] runner test not using 08MQ as example anymore

  bclenet

  committed
  988e536

  Copy full SHA for 988e536

• Issue with SelectFiles' base_directory

  bclenet

  committed
  ffcdf6e

  Copy full SHA for ffcdf6e

• Towards a running version of the pipeline

  bclenet

  committed
  04d835e

  Copy full SHA for 04d835e

• [TEST] stop using 08MQ in tests

  bclenet

  committed
  7525309

  Copy full SHA for 7525309

Commits on Oct 16, 2023

• 08MQ preprocessing instantiable

  bclenet

  committed
  da82396

  Copy full SHA for da82396

Commits on Oct 17, 2023

• Compute confounds node

  bclenet

  committed
  8fd2195

  Copy full SHA for 8fd2195

• Group analysis workflow bug

  bclenet

  committed
  9a63118

  Copy full SHA for 9a63118

• Group analysis workflow bug

  bclenet

  committed
  95fe702

  Copy full SHA for 95fe702

• Group analysis workflow bug

  bclenet

  committed
  1ac7267

  Copy full SHA for 1ac7267

• Issue with Registration and Threshold

  bclenet

  committed
  ecc4977

  Copy full SHA for ecc4977

• Bug with shrink factors

  bclenet

  committed
  d2cd3e4

  Copy full SHA for d2cd3e4

• Bug with shrink factors

  bclenet

  committed
  0f186a8

  Copy full SHA for 0f186a8

• Bug with shrink factors

  bclenet

  committed
  2c73712

  Copy full SHA for 2c73712

Commits on Oct 18, 2023

• ANTs registration [skip ci]

  bclenet

  committed
  8dba3d3

  Copy full SHA for 8dba3d3

• Testing parameters for antsRegistration [skip ci]

  bclenet

  committed
  7371a95

  Copy full SHA for 7371a95

Commits on Oct 20, 2023

• Inverse coregistration transform [skip ci]

  bclenet

  committed
  82c4f0a

  Copy full SHA for 82c4f0a

• Inverse coregistration transform [skip ci]

  bclenet

  committed
  6495767

  Copy full SHA for 6495767

• Compute confounds parameterization [skip ci]

  bclenet

  committed
  818de15

  Copy full SHA for 818de15

• ANTs composite transform [skip ci]

  bclenet

  committed
  735d2f7

  Copy full SHA for 735d2f7

Commits on Oct 23, 2023

• Trying ANTs' ApplyTransforms

  bclenet

  committed
  a1eb020

  Copy full SHA for a1eb020

• Preprocessing outputs [skip ci]

  bclenet

  committed
  3f61b5d

  Copy full SHA for 3f61b5d

• Preprocessing outputs [skip ci]

  bclenet

  committed
  09111a5

  Copy full SHA for 09111a5

• Add smoothing [skip ci]

  bclenet

  committed
  cde9f37

  Copy full SHA for cde9f37

• Motion correction outputs [skip ci]

  bclenet

  committed
  098de9f

  Copy full SHA for 098de9f

• Parse segmentation maps [skip ci]

  bclenet

  committed
  a335fd6

  Copy full SHA for a335fd6

• Use partial volume files from segmentation [skip ci]

  bclenet

  committed
  7579d53

  Copy full SHA for 7579d53

• Use partial volume files from segmentation [skip ci]

  bclenet

  committed
  d26e188

  Copy full SHA for d26e188

• First try of run level analysis [skip ci]

  bclenet

  committed
  23d3af9

  Copy full SHA for 23d3af9

• First try of run level analysis [skip ci]

  bclenet

  committed
  6dfc51f

  Copy full SHA for 6dfc51f

• First try of run level analysis [skip ci]

  bclenet

  committed
  4adfe43

  Copy full SHA for 4adfe43

• First try of run level analysis [skip ci]

  bclenet

  committed
  af08110

  Copy full SHA for af08110

• First try of run level analysis [skip ci]

  bclenet

  committed
  dbfed24

  Copy full SHA for dbfed24

• First try of run level analysis [skip ci]

  bclenet

  committed
  d2951b3

  Copy full SHA for d2951b3

• First try of run level analysis [skip ci]

  bclenet

  committed
  1e46ec0

  Copy full SHA for 1e46ec0

• First try of run level analysis [skip ci]

  bclenet

  committed
  3fe4ca2

  Copy full SHA for 3fe4ca2

• First try of run level analysis [skip ci]

  bclenet

  committed
  72635b1

  Copy full SHA for 72635b1

• ANT's apply transform bug [skip ci]

  bclenet

  committed
  4c62bf2

  Copy full SHA for 4c62bf2

• ANT's apply transform bug [skip ci]

  bclenet

  committed
  e7217da

  Copy full SHA for e7217da

Commits on Oct 24, 2023

• ANT's apply transform bug [skip ci]

  bclenet

  committed
  e029f37

  Copy full SHA for e029f37

• ANT's apply transform bug [skip ci]

  bclenet

  committed
  e8f475d

  Copy full SHA for e8f475d

• ANT's apply transform bug [skip ci]

  bclenet

  committed
  04bdeba

  Copy full SHA for 04bdeba

• First try of run level analysis [skip ci]

  bclenet

  committed
  858004a

  Copy full SHA for 858004a

• First try of run level analysis [skip ci]

  bclenet

  committed
  b63a052

  Copy full SHA for b63a052

• First try of subject level analysis [skip ci]

  bclenet

  committed
  8ba967f

  Copy full SHA for 8ba967f

• First try of subject level analysis [skip ci]

  bclenet

  committed
  d39fc44

  Copy full SHA for d39fc44

• FSL's Merge disambiguataion [skip ci]

  bclenet

  committed
  98abcfc

  Copy full SHA for 98abcfc

• Use MNI masks [skip ci]

  bclenet

  committed
  77515c0

  Copy full SHA for 77515c0

• Preprocessing sieable files removing

  bclenet

  committed
  8d907cd

  Copy full SHA for 8d907cd

• Bug with contrasts Node naming

  bclenet

  committed
  1ea7e12

  Copy full SHA for 1ea7e12

Commits on Oct 25, 2023

• Base directories

  bclenet

  committed
  e79239f

  Copy full SHA for e79239f

• Remove alignment_func_to_mni's output [skip ci]

  bclenet

  committed
  4dad129

  Copy full SHA for 4dad129

• Autoremove intermediate results [skip ci]

  bclenet

  committed
  26ddc3a

  Copy full SHA for 26ddc3a

• Autoremove intermediate results [skip ci]

  bclenet

  committed
  bedc2b5

  Copy full SHA for bedc2b5

• Revert "Remove alignment_func_to_mni's output [skip ci]"

  Show description for fa2ebd7
  bclenet

  committed
  fa2ebd7

  Copy full SHA for fa2ebd7

• Bug after revert [skip ci]

  bclenet

  committed
  7832af2

  Copy full SHA for 7832af2

• Bug after revert [skip ci]

  bclenet

  committed
  c575158

  Copy full SHA for c575158

Commits on Oct 26, 2023

• [TEST] tests updates

  bclenet

  committed
  f6844a5

  Copy full SHA for f6844a5

• Bug with big files removal

  bclenet

  committed
  ed4f11e

  Copy full SHA for ed4f11e

Commits on Oct 27, 2023

• Deletinglarge files after datasink

  bclenet

  committed
  8770d81

  Copy full SHA for 8770d81

Commits on Nov 15, 2023

• [BUG] group level workflow connections [skip ci]

  bclenet

  committed
  8992184

  Copy full SHA for 8992184

• [BUG] group level [skip ci]

  bclenet

  committed
  f488a7b

  Copy full SHA for f488a7b

• [REFAC] equalRange > equal_range [skip ci]

  bclenet

  committed
  d93e3a6

  Copy full SHA for d93e3a6

• Regressors function + group output [skip ci]

  bclenet

  committed
  bd13c53

  Copy full SHA for bd13c53

• Typo in regressors [skip ci]

  bclenet

  committed
  0f8f35e

  Copy full SHA for 0f8f35e

• Issue with list of regressors [skip ci]

  bclenet

  committed
  3025305

  Copy full SHA for 3025305

• Issue with list of regressors [skip ci]

  bclenet

  committed
  8d14472

  Copy full SHA for 8d14472

• Issue with list of regressors [skip ci]

  bclenet

  committed
  817ec31

  Copy full SHA for 817ec31

• [TEST] adding unit tests to 08MQ [skip ci]

  bclenet

  committed
  e092bc5

  Copy full SHA for e092bc5

• [TEST] typo [skip ci]

  bclenet

  committed
  4892f5c

  Copy full SHA for 4892f5c

• [TEST] static methods testing [skip ci]

  bclenet

  committed
  517fc41

  Copy full SHA for 517fc41

• [TEST] adding unit tests for 08MQ

  bclenet

  committed
  fd9bbf3

  Copy full SHA for fd9bbf3

• [CODESPELL] typos

  bclenet

  committed
  7252864

  Copy full SHA for 7252864

Commits on Nov 16, 2023

• [BUG] inversion between groups [skip ci]

  bclenet

  committed
  68adef4

  Copy full SHA for 68adef4

Commits on Nov 20, 2023

• Merge branch 'Inria-Empenn:main' into main

  bclenet

  authored
  c03e9d1

  Copy full SHA for c03e9d1

• Merge branch 'main' into 08MQ_reproduction

  bclenet

  committed
  e7e9f48

  Copy full SHA for e7e9f48

• [REFAC] Using narps_open.core functions

  bclenet

  committed
  c6ae521

  Copy full SHA for c6ae521

• [REFAC] using narps_open.core functions [TEST] events data in a file

  bclenet

  committed
  7433106

  Copy full SHA for 7433106

Commits on Nov 21, 2023

• [BUG] remove_file input naming [skip ci]

  bclenet

  committed
  053d72c

  Copy full SHA for 053d72c

Commits on Nov 22, 2023

• [BUG] remove sub- from participants id [skip ci]

  bclenet

  committed
  34b649e

  Copy full SHA for 34b649e

• [BUG] typo in get_two_sample_t_test_regressors inputs [skip ci]

  bclenet

  committed
  9700166

  Copy full SHA for 9700166

Commits on Nov 28, 2023

• Compute brightness threshold for SUSAN [skip ci]

  bclenet

  committed
  8c73773

  Copy full SHA for 8c73773

• Use ANTs ApplyTransforms for alignment_func_to_anat Node [skip ci]

  bclenet

  committed
  8e736f7

  Copy full SHA for 8e736f7

Commits on Nov 29, 2023

• [narps_open.core] adding list_to_file function [skip ci]

  bclenet

  committed
  36e8fdd

  Copy full SHA for 36e8fdd

• [08MQ] custom timings as input of SliceTimer [skip ci]

  bclenet

  committed
  b979f1c

  Copy full SHA for b979f1c

Commits on Nov 30, 2023

• Typo preprocessing

  bclenet

  committed
  839e53d

  Copy full SHA for 839e53d

Commits on Dec 5, 2023

• Computing masks : output of preprocessing [skip ci]

  bclenet

  committed
  153e747

  Copy full SHA for 153e747

• Computing masks : output of preprocessing [skip ci]

  bclenet

  committed
  01bfb8e

  Copy full SHA for 01bfb8e

• Back to ApplyXFM, with no_resample option [skip ci]

  bclenet

  committed
  9a16b06

  Copy full SHA for 9a16b06

• Back to ApplyXFM, with no_resample option [skip ci]

  bclenet

  committed
  502c206

  Copy full SHA for 502c206

• Back to ApplyXFM, with no_resample option [skip ci]

  bclenet

  committed
  8adcf86

  Copy full SHA for 8adcf86

• Mask intersection of func as input of subject_level estimate model [skip ci]

  bclenet

  committed
  eb8ae1c

  Copy full SHA for eb8ae1c

• Mask intersection of func as input of subject_level estimate model [skip ci]

  bclenet

  committed
  2789d44

  Copy full SHA for 2789d44

• Mask intersection in group_level analysis [skip ci]

  bclenet

  committed
  5e02694

  Copy full SHA for 5e02694

Commits on Dec 6, 2023

• Mask input + mask intersection inside group level analysis [skip ci]

  bclenet

  committed
  26f0e09

  Copy full SHA for 26f0e09

• Adding mask to randomise Node [skip ci]

  bclenet

  committed
  8ac81d1

  Copy full SHA for 8ac81d1

Commits on Dec 11, 2023

• Actually passing mask tu compute median node [skip ci]

  bclenet

  committed
  ad0b24f

  Copy full SHA for ad0b24f

• Actually passing mask tu compute median node [skip ci]

  bclenet

  committed
  cb99973

  Copy full SHA for cb99973

• Actually passing mask tu compute median node [skip ci]

  bclenet

  committed
  09cfe2f

  Copy full SHA for 09cfe2f

• Adding mask to compute median node [skip ci]

  bclenet

  committed
  bfd163e

  Copy full SHA for bfd163e

Commits on Dec 12, 2023

• Adding wm sgmentation to coregistration_sbref node working with bbr cost function [skip ci]

  bclenet

  committed
  7f5191c

  Copy full SHA for 7f5191c

• Adding brain extraction of sbrefs [skip ci]

  bclenet

  committed
  d83d066

  Copy full SHA for d83d066

• Using unthresholded wm for coregistration_sbref node [skip ci]

  bclenet

  committed
  86da1a1

  Copy full SHA for 86da1a1

• Bug with WM selection [skip ci]

  bclenet

  committed
  483a4d0

  Copy full SHA for 483a4d0

• Adding back remove functions for testing on 20 subjects [skip ci]

  bclenet

  committed
  843eb1f

  Copy full SHA for 843eb1f

Commits on Dec 18, 2023

• Removing more intermediate results [skip ci]

  bclenet

  committed
  e0f599f

  Copy full SHA for e0f599f

Commits on Dec 20, 2023

• Force 2.0mm resampling for alignment_func_to_anat node [skip ci]

  bclenet

  committed
  6c228f9

  Copy full SHA for 6c228f9

• Force 2.0mm resampling for alignment_func_to_anat node [skip ci]

  bclenet

  committed
  40a67e1

  Copy full SHA for 40a67e1

• [TEST][PEP8] [skip ci]

  bclenet

  committed
  3250a6d

  Copy full SHA for 3250a6d