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51PW reproduction #134

Merged
merged 154 commits into from
Feb 12, 2024
Merged

51PW reproduction #134

merged 154 commits into from
Feb 12, 2024

Commits on Aug 31, 2023

  1. [BUG] inside unit_tests workflow

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  2. Merge branch 'Inria-Empenn:main' into main

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Commits on Sep 4, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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Commits on Sep 19, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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Commits on Sep 21, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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Commits on Sep 29, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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  2. Merge branch 'Inria-Empenn:main' into main

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  3. Merge branch 'Inria-Empenn:main' into main

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Commits on Oct 5, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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  2. Merge branch 'Inria-Empenn:main' into main

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Commits on Oct 6, 2023

  1. [08MQ] Preprocessing script in progress

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Commits on Oct 9, 2023

  1. Working on preprocessing

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  2. Codespell

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Commits on Oct 10, 2023

  1. Working on pipeline 08MQ

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  2. Merge branch 'Inria-Empenn:main' into main

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Commits on Oct 11, 2023

  1. Towards a running version of the pipeline

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  2. Conforming to Pipeline class + init test module

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  3. Merge branch 'main' into 08MQ_reproduction

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  4. Towards a running version of the pipeline

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  5. Towards a running version of the pipeline

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Commits on Oct 13, 2023

  1. Towards a running version of the pipeline

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

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  3. Issue with SelectFiles' base_directory

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  4. Towards a running version of the pipeline

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  5. [TEST] stop using 08MQ in tests

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Commits on Oct 16, 2023

  1. 08MQ preprocessing instantiable

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Commits on Oct 17, 2023

  1. Compute confounds node

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  2. Group analysis workflow bug

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  3. Group analysis workflow bug

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  4. Group analysis workflow bug

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  5. Issue with Registration and Threshold

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  6. Bug with shrink factors

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  7. Bug with shrink factors

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  8. Bug with shrink factors

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Commits on Oct 18, 2023

  1. ANTs registration [skip ci]

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  2. Testing parameters for antsRegistration [skip ci]

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Commits on Oct 20, 2023

  1. Inverse coregistration transform [skip ci]

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  2. Inverse coregistration transform [skip ci]

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  3. Compute confounds parameterization [skip ci]

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  4. ANTs composite transform [skip ci]

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Commits on Oct 23, 2023

  1. Trying ANTs' ApplyTransforms

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  2. Preprocessing outputs [skip ci]

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  3. Preprocessing outputs [skip ci]

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  4. Add smoothing [skip ci]

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  5. Motion correction outputs [skip ci]

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  6. Parse segmentation maps [skip ci]

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  7. Use partial volume files from segmentation [skip ci]

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  8. Use partial volume files from segmentation [skip ci]

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  9. First try of run level analysis [skip ci]

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  10. First try of run level analysis [skip ci]

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  11. First try of run level analysis [skip ci]

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  12. First try of run level analysis [skip ci]

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  13. First try of run level analysis [skip ci]

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  14. First try of run level analysis [skip ci]

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  15. First try of run level analysis [skip ci]

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  16. First try of run level analysis [skip ci]

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  17. First try of run level analysis [skip ci]

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  18. ANT's apply transform bug [skip ci]

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  19. ANT's apply transform bug [skip ci]

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Commits on Oct 24, 2023

  1. ANT's apply transform bug [skip ci]

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  2. ANT's apply transform bug [skip ci]

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  3. ANT's apply transform bug [skip ci]

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  4. First try of run level analysis [skip ci]

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  5. First try of run level analysis [skip ci]

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  6. First try of subject level analysis [skip ci]

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  7. First try of subject level analysis [skip ci]

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  8. FSL's Merge disambiguataion [skip ci]

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  9. Use MNI masks [skip ci]

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  10. Preprocessing sieable files removing

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  11. Bug with contrasts Node naming

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Commits on Oct 25, 2023

  1. Base directories

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  2. Remove alignment_func_to_mni's output [skip ci]

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  3. Autoremove intermediate results [skip ci]

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  4. Autoremove intermediate results [skip ci]

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  5. Revert "Remove alignment_func_to_mni's output [skip ci]" 

    This reverts commit 4dad129.
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  6. Bug after revert [skip ci]

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  7. Bug after revert [skip ci]

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Commits on Oct 26, 2023

  1. [TEST] tests updates

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  2. Bug with big files removal

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Commits on Oct 27, 2023

  1. Deletinglarge files after datasink

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Commits on Nov 15, 2023

  1. [BUG] group level workflow connections [skip ci]

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  2. [BUG] group level [skip ci]

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  3. [REFAC] equalRange > equal_range [skip ci]

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  4. Regressors function + group output [skip ci]

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  5. Typo in regressors [skip ci]

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  6. Issue with list of regressors [skip ci]

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  7. Issue with list of regressors [skip ci]

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  8. Issue with list of regressors [skip ci]

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  9. [TEST] adding unit tests to 08MQ [skip ci]

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  10. [TEST] typo [skip ci]

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  11. [TEST] static methods testing [skip ci]

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  12. [TEST] adding unit tests for 08MQ

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  13. [CODESPELL] typos

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Commits on Nov 16, 2023

  1. [BUG] inversion between groups [skip ci]

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Commits on Nov 20, 2023

  1. Merge branch 'Inria-Empenn:main' into main

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  2. Merge branch 'main' into 08MQ_reproduction

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  3. [REFAC] Using narps_open.core functions

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

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Commits on Nov 21, 2023

  1. [BUG] remove_file input naming [skip ci]

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Commits on Nov 22, 2023

  1. [BUG] remove sub- from participants id [skip ci]

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  2. [BUG] typo in get_two_sample_t_test_regressors inputs [skip ci]

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  3. Merge branch 'Inria-Empenn:main' into main

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  4. Merge branch 'Inria-Empenn:main' into main

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Commits on Nov 28, 2023

  1. Compute brightness threshold for SUSAN [skip ci]

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  2. Use ANTs ApplyTransforms for alignment_func_to_anat Node [skip ci]

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Commits on Nov 29, 2023

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

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  2. [08MQ] custom timings as input of SliceTimer [skip ci]

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Commits on Nov 30, 2023

  1. Typo preprocessing

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    bclenet committed Nov 30, 2023
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Commits on Dec 5, 2023

  1. Computing masks : output of preprocessing [skip ci]

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    bclenet committed Dec 5, 2023
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  2. Computing masks : output of preprocessing [skip ci]

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    bclenet committed Dec 5, 2023
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  3. Back to ApplyXFM, with no_resample option [skip ci]

    @bclenet
    bclenet committed Dec 5, 2023
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  4. Back to ApplyXFM, with no_resample option [skip ci]

    @bclenet
    bclenet committed Dec 5, 2023
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  5. Back to ApplyXFM, with no_resample option [skip ci]

    @bclenet
    bclenet committed Dec 5, 2023
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  6. Mask intersection of func as input of subject_level estimate model [s… 

    …kip ci]
    @bclenet
    bclenet committed Dec 5, 2023
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  7. Mask intersection of func as input of subject_level estimate model [s… 

    …kip ci]
    @bclenet
    bclenet committed Dec 5, 2023
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  8. Mask intersection in group_level analysis [skip ci]

    @bclenet
    bclenet committed Dec 5, 2023
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Commits on Dec 6, 2023

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

    @bclenet
    bclenet committed Dec 6, 2023
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  2. Adding mask to randomise Node [skip ci]

    @bclenet
    bclenet committed Dec 6, 2023
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Commits on Dec 11, 2023

  1. Actually passing mask tu compute median node [skip ci]

    @bclenet
    bclenet committed Dec 11, 2023
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  2. Actually passing mask tu compute median node [skip ci]

    @bclenet
    bclenet committed Dec 11, 2023
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  3. Actually passing mask tu compute median node [skip ci]

    @bclenet
    bclenet committed Dec 11, 2023
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  4. Adding mask to compute median node [skip ci]

    @bclenet
    bclenet committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. Adding wm sgmentation to coregistration_sbref node working with bbr c… 

    …ost function [skip ci]
    @bclenet
    bclenet committed Dec 12, 2023
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  2. Adding brain extraction of sbrefs [skip ci]

    @bclenet
    bclenet committed Dec 12, 2023
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  3. Using unthresholded wm for coregistration_sbref node [skip ci]

    @bclenet
    bclenet committed Dec 12, 2023
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  4. Bug with WM selection [skip ci]

    @bclenet
    bclenet committed Dec 12, 2023
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  5. Adding back remove functions for testing on 20 subjects [skip ci]

    @bclenet
    bclenet committed Dec 12, 2023
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Commits on Dec 18, 2023

  1. Removing more intermediate results [skip ci]

    @bclenet
    bclenet committed Dec 18, 2023
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Commits on Dec 20, 2023

  1. First version of the pipeline [skip ci]

    @bclenet
    bclenet committed Dec 20, 2023
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  2. Force 2.0mm resampling for alignment_func_to_anat node [skip ci]

    @bclenet
    bclenet committed Dec 20, 2023
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  3. Force 2.0mm resampling for alignment_func_to_anat node [skip ci]

    @bclenet
    bclenet committed Dec 20, 2023
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  4. [TEST][PEP8] [skip ci]

    @bclenet
    bclenet committed Dec 20, 2023
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  5. Preprocessing done [skip ci]

    @bclenet
    bclenet committed Dec 20, 2023
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  6. Adding test features into 51PW_reproduction

    @bclenet
    bclenet committed Dec 20, 2023
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  7. [TEST] updating test for 51PW

    @bclenet
    bclenet committed Dec 20, 2023
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Commits on Jan 5, 2024

  1. Merge branch 'Inria-Empenn:main' into main

    @bclenet
    bclenet authored Jan 5, 2024
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Commits on Jan 10, 2024

  1. Merge branch 'Inria-Empenn:main' into main

    @bclenet
    bclenet authored Jan 10, 2024
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Commits on Jan 11, 2024

  1. Merge branch 'Inria-Empenn:main' into main

    @bclenet
    bclenet authored Jan 11, 2024
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  2. [DATALAD] change results url

    @bclenet
    bclenet committed Jan 11, 2024
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  3. Merge pull request #3 from bclenet/results 

    [DATALAD] change results url
    @bclenet
    bclenet authored Jan 11, 2024
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Commits on Jan 15, 2024

  1. Merge branch 'main' into 51PW_reproduction

    @bclenet
    bclenet committed Jan 15, 2024
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Commits on Jan 18, 2024

  1. [BUG] select files in run level analysis

    @bclenet
    bclenet committed Jan 18, 2024
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  2. [BUG] find mask name in run-level analysis

    @bclenet
    bclenet committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. Remove autoregressive model fitting

    @bclenet
    bclenet committed Jan 19, 2024
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Commits on Jan 29, 2024

  1. Merge branch 'main' into 51PW_reproduction

    @bclenet
    bclenet committed Jan 29, 2024
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  2. Remove large files

    @bclenet
    bclenet committed Jan 29, 2024
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Commits on Jan 31, 2024

  1. Bugs after remove file section

    @bclenet
    bclenet committed Jan 31, 2024
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  2. Merge branch 'main' into 51PW_reproduction

    @bclenet
    bclenet committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. Remove outputs

    @bclenet
    bclenet committed Feb 1, 2024
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  2. [TEST] test pipeline outputs for 51PW [skip ci]

    @bclenet
    bclenet committed Feb 1, 2024
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  3. [TEST] test pipeline outputs for 51PW [skip ci]

    @bclenet
    bclenet committed Feb 1, 2024
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  4. Output paths

    @bclenet
    bclenet committed Feb 1, 2024
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Commits on Feb 7, 2024

  1. Merge branch 'main' into 51PW_reproduction

    @bclenet
    bclenet committed Feb 7, 2024
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  2. Mask names

    @bclenet
    bclenet committed Feb 7, 2024
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