automaticanalysis/automaticanalysis: Release 5.8.0

This release contains numerous changes to make the code self-sufficient and improve robustness and useability. It also implements an efficient CI/CD framework based on GitHub Actions and GitHub-hosted runners to facilitate development.

New generic features

• _aatoolbox interface for transparent integration of the toolboxes
• Tiered examples (tutorials and demonstrations), which runs out-of-box

New features for fMRI

• Psycho-Physiological Interaction
• Frame censoring
• ICA-AROMA
• Integration of the CONN toolbox
• Integration of The Decoding Toolbox (also for connectivity)

New features for M/EEG

• Integration on EEGLAB and FieldTrip toolboxes
• New sets of modules based on EEGLAB and FieldTrip
• Time-lock, time-frequency, connectivity, and cross-frequency analyses
• Sensor- and source-level analyses
• Demonstration example

• PR from tiborauer by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/94
• V5 devel by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/101
• UPDATE: aamod_coreg_extended_1 (T1 to MNI, within-modality) uses ncc as default cost function by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/102
• DEBUG: incomplete meminfo update by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/106
• volumes2movie: replaced depreciated movie2avi with writeVideo by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/108
• UPDATE: local parallel (by slices) execution switched from parpool to… by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/107
• Resynch by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/112
• Minor fixes from our forked repo by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/114
• BIDS import/export, bet_premask bug fix, new modules by @jooh in https://github.com/automaticanalysis/automaticanalysis/pull/115
• re-branching, special_session, MPM by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/117
• Major revisions to aaq_qsub (already merged with main branch) by @dprice80 in https://github.com/automaticanalysis/automaticanalysis/pull/119
• UPDATE: MPM and DKIToolbox by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/121
• Dprice80 empty mask patch by @dprice80 in https://github.com/automaticanalysis/automaticanalysis/pull/129
• Fix bug: error in last module not stopping by @dprice80 in https://github.com/automaticanalysis/automaticanalysis/pull/136
• aas_addsubject & diffusion (with topup) by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/131
• Removed try catch blocks from meg modules by @dprice80 in https://github.com/automaticanalysis/automaticanalysis/pull/138
• WashU code changes for merging by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/124
• GE (UEA) pipeline (fieldmap, diffusion, fmri) and other improvements to increase non-CBSU usability by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/137
• CLEANUP: removed deprecated and unused modules by @jpeelle in https://github.com/automaticanalysis/automaticanalysis/pull/148
• Tibor by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/149
• Tibor by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/151
• documentation for special sessions by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/158
• PR161 + review by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/163
• Refactor example scripts for portability, implement basic automated testing by @jooh in https://github.com/automaticanalysis/automaticanalysis/pull/161
• Improvements to first and second level thresholding by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/159
• CLEANUP: Removed Windows line breaks by @jpeelle in https://github.com/automaticanalysis/automaticanalysis/pull/172
• fix for selected sessions bug by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/174
• code changes to handle single-file dicom and a new TR/TE header field by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/180
• Improvements and debugs by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/173
• minor bugfixes on aa_export_toBIDS by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/196
• Specific debugs and update local settings by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/198
• stream renaming support for camcan, big debug, Tibor PRs by @jooh in https://github.com/automaticanalysis/automaticanalysis/pull/205
• Quick debugs by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/204
• non_DCS for Slurm scheduler (University of Surrey) by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/203
• Philips new format + debugs by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/202
• DEBUGS by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/209
• added acq_details options by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/211
• aacache, toolboxes by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/213
• M/EEG by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/216
• QUICK DEBUG by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/218
• CLEANUP - modulenames by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/221
• new aa_test and developer tools by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/240
• aa 5.6.0 by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/246
• Merge qsub remodel by @hhentschke in https://github.com/automaticanalysis/automaticanalysis/pull/250
• 5.7.0 by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/255
• New denoising modules and miscellaneous fixes by @jones-michael-s in https://github.com/automaticanalysis/automaticanalysis/pull/262
• New denoising modules and miscellaneous fixes from WASHU by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/274
• Bugfixes related to Getting started by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/263
• Fix aas_checkpath allowcolon input effect by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/268
• Fix validatepaths chararray by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/270
• tidy aamod_coreg_extended_2_epi.xml by @ethanknights in https://github.com/automaticanalysis/automaticanalysis/pull/283
• New tests from WASHU by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/292
• 5.7.0 by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/273
• Fixes to be able to run example helloworld on windows by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/291
• Smallfixes by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/293
• Feature cleaner defaults and examples by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/298
• ENH: Adapt aa_test to use matlab unittest framework by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/303
• Feature: dedicated user parameters creation by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/302
• Fix report by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/300
• ENH - MEEG atlasing by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/307
• Feature downloaddemo rework and tests by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/306
• FIX - denorm and roi processing >1 inputs by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/308
• ENH - epireg by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/309
• TDT by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/310
• Windows example spm by @AljenU in https://github.com/automaticanalysis/automaticanalysis/pull/315
• FIX - BWT in parametersets by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/316
• Registration by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/317
• Meeg demo by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/318

• @jones-michael-s made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/108
• @dprice80 made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/119
• @jpeelle made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/148
• @hhentschke made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/250
• @AljenU made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/263
• @ethanknights made their first contribution in https://github.com/automaticanalysis/automaticanalysis/pull/283

Full Changelog: https://github.com/automaticanalysis/automaticanalysis/compare/v5.4.0...v5.8.0