Automatic Analysis 5.8.1

What's Changed

• ENH - EEGLAB with safe plugins by @tiborauer in #324
• FIX - DARTEL by @tiborauer in #325

Full Changelog: v5.8.0...v5.8.1

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

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

New Contributors

• @jones-michael-s made their first contribution in #108
• @dprice80 made their first contribution in #119
• @jpeelle made their first contribution in #148
• @hhentschke made their first contribution in #250
• @AljenU made their first contribution in #263
• @ethanknights made their first contribution in #283

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

Release 5.0.0

As the change in the major versioning implies, older user master scripts are not compatible with v5. Examples has been updated to demonstrate new syntax. In addition, pipelines processed with older versions cannot be re-processed with v5 (aap structure stored in aap_parameters.mat is not compatible). A script aa_convert_subjects is provided to convert aap structure stored in aap_parameters.mat. When connecting to a remote pipeline processed with an older version of aa, aa_convert_subjects is automatically called; so no explicit conversion is required.

New general features

• More detailed documentation of several key functions
• Explicit subject identifier aap.acq_details.subjects.subjname: aas_addsubject
  • Subject name is more unambiguously specified
  • Subject name is not tied to the data
  • Same subject name can be used as a reference in the whole UMS
• Longitudinal/multi-visit measurement
• In case of selected_session, only relevant inputs will be retrieved
• Session-specific fieldmaps
• aas_addsubject has a more intuitive parameterisation
• From NIfTI
  • BIDS datasets are supported (full)
• Reporting remote pipeline
• Lightweighting: remove ANTs, VBM8 and FreeSurfer deface templates from the package and mark them as (optional) requirements

New features for structural

• aamod_mask_fromsegment accepts different exact thresholds for GM, WM, CSF

New features for fMRI

• Reorienting input images (structural, diffusion and EPI) to their middle voxel (aamod_reorienttomiddle_*)
• Specifying contrast for certain sessions using format "sessions:[+[...]]"
• Specifying contrast with condition names in a format x<main ('m') or parametric ('p')><number of basis/parametric function>. N.B.: It requires regressor names with UPPERCASE letters only!

Bugfixes

• Scaling automatic temporal modulation
• aamod_bet_meanepi
• aamod_waveletdespike using explicit brainmask

Release 4.3.1

4.3.1

Bugfix

• Exmaple user master script and tasklist are provided for demo dataset: (aa_user_demo_v2)
• Compatibility with MATLAB r2015b

Release 4.21

Please use v4.21, which contains minor bug fixes.

Release 4.20

This stable release corresponds to the version described in our manuscript

Please cite this in any publications that use aa
Cusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, Peelle JE (2015) Automatic analysis (aa): Efficient neuroimaging workflows and parallel processing using Matlab and XML. Frontiers in Neuroinformatics 8:90.

v4.10

Update aaworker_getparmpath.m