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51PW reproduction (#134)
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* [BUG] inside unit_tests workflow

* [08MQ] Preprocessing script in progress

* Working on preprocessing

* Codespell

* Working on pipeline 08MQ

* Towards a running version of the pipeline

* Conforming to Pipeline class + init test module

* Towards a running version of the pipeline

* Towards a running version of the pipeline

* Towards a running version of the pipeline

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

* Issue with SelectFiles' base_directory

* Towards a running version of the pipeline

* [TEST] stop using 08MQ in tests

* 08MQ preprocessing instantiable

* Compute confounds node

* Group analysis workflow bug

* Group analysis workflow bug

* Group analysis workflow bug

* Issue with Registration and Threshold

* Bug with shrink factors

* Bug with shrink factors

* Bug with shrink factors

* ANTs registration [skip ci]

* Testing parameters for antsRegistration [skip ci]

* Inverse coregistration transform [skip ci]

* Inverse coregistration transform [skip ci]

* Compute confounds parameterization [skip ci]

* ANTs composite transform [skip ci]

* Trying ANTs' ApplyTransforms

* Preprocessing outputs [skip ci]

* Preprocessing outputs [skip ci]

* Add smoothing [skip ci]

* Motion correction outputs [skip ci]

* Parse segmentation maps [skip ci]

* Use partial volume files from segmentation [skip ci]

* Use partial volume files from segmentation [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* ANT's apply transform bug [skip ci]

* ANT's apply transform bug [skip ci]

* ANT's apply transform bug [skip ci]

* ANT's apply transform bug [skip ci]

* ANT's apply transform bug [skip ci]

* First try of run level analysis [skip ci]

* First try of run level analysis [skip ci]

* First try of subject level analysis [skip ci]

* First try of subject level analysis [skip ci]

* FSL's Merge disambiguataion [skip ci]

* Use MNI masks [skip ci]

* Preprocessing sieable files removing

* Bug with contrasts Node naming

* Base directories

* Remove alignment_func_to_mni's output [skip ci]

* Autoremove intermediate results [skip ci]

* Autoremove intermediate results [skip ci]

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

This reverts commit 4dad129.

* Bug after revert [skip ci]

* Bug after revert [skip ci]

* [TEST] tests updates

* Bug with big files removal

* Deletinglarge files after datasink

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

* [BUG] group level [skip ci]

* [REFAC] equalRange > equal_range [skip ci]

* Regressors function + group output [skip ci]

* Typo in regressors [skip ci]

* Issue with list of  regressors [skip ci]

* Issue with list of  regressors [skip ci]

* Issue with list of  regressors [skip ci]

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

* [TEST] typo [skip ci]

* [TEST] static methods testing [skip ci]

* [TEST] adding unit tests for 08MQ

* [CODESPELL] typos

* [BUG] inversion between groups [skip ci]

* [REFAC] Using narps_open.core functions

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

* [BUG] remove_file input naming [skip ci]

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

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

* Compute brightness threshold for SUSAN [skip ci]

* Use ANTs ApplyTransforms for alignment_func_to_anat Node [skip ci]

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

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

* Typo preprocessing

* Computing masks : output of preprocessing [skip ci]

* Computing masks : output of preprocessing [skip ci]

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

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

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

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

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

* Mask intersection in group_level analysis [skip ci]

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

* Adding mask to randomise Node [skip ci]

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

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

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

* Adding mask to compute median node [skip ci]

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

* Adding brain extraction of sbrefs [skip ci]

* Using unthresholded wm for coregistration_sbref node [skip ci]

* Bug with WM selection [skip ci]

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

* Removing more intermediate results [skip ci]

* First version of the pipeline [skip ci]

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

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

* [TEST][PEP8] [skip ci]

* Preprocessing done [skip ci]

* [TEST] updating test for 51PW

* [DATALAD] change results url

* [BUG] select files in run level analysis

* [BUG] find mask name in run-level analysis

* Remove autoregressive model fitting

* Remove large files

* Bugs after remove file section

* Remove outputs

* [TEST] test pipeline outputs for 51PW [skip ci]

* [TEST] test pipeline outputs for 51PW [skip ci]

* Output paths

* Mask names
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bclenet authored Feb 12, 2024
1 parent 8ae3645 commit 947a71d
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Showing 3 changed files with 1,097 additions and 1 deletion.
2 changes: 1 addition & 1 deletion narps_open/pipelines/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
'4SZ2': None,
'4TQ6': None,
'50GV': None,
'51PW': None,
'51PW': 'PipelineTeam51PW',
'5G9K': None,
'6FH5': None,
'6VV2': None,
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