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51PW reproduction (Inria-Empenn#134)
* [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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