Release 5.8.0 #323

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

• aa_toolbox 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

What's Changed

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

New Contributors

• @jones-michael-s made their first contribution in volumes2movie: replaced depreciated movie2avi with writeVideo #108
• @dprice80 made their first contribution in Major revisions to aaq_qsub (already merged with main branch) #119
• @jpeelle made their first contribution in CLEANUP: removed deprecated and unused modules #148
• @hhentschke made their first contribution in Merge qsub remodel #250
• @AljenU made their first contribution in Bugfixes related to Getting started #263
• @ethanknights made their first contribution in tidy aamod_coreg_extended_2_epi.xml #283

Full Changelog: v5.4.0...v5.8.0