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Recent Releases of automaticanalysis

automaticanalysis - Automatic Analysis 5.8.1

What's Changed

  • ENH - EEGLAB with safe plugins by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/324
  • FIX - DARTEL by @tiborauer in https://github.com/automaticanalysis/automaticanalysis/pull/325

Full Changelog: https://github.com/automaticanalysis/automaticanalysis/compare/v5.8.0...v5.8.1

- MATLAB
Published by tiborauer almost 4 years ago

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

What's Changed

  • 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: aamodcoregextended_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 aaexporttoBIDS 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 aamodcoregextended2epi.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

New Contributors

  • @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

- MATLAB
Published by tiborauer about 4 years ago

automaticanalysis - 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 aapparameters.mat_ is not compatible). A script aa_convert_subjects is provided to convert aap structure stored in aapparameters.mat. When connecting to a remote pipeline processed with an older version of aa, `aaconvert_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

  • aamodmaskfromsegment 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
    . N.B.: It requires regressor names with UPPERCASE letters only!

Bugfixes

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

- MATLAB
Published by tiborauer almost 10 years ago

automaticanalysis - Release 4.3.1

4.3.1

Bugfix

- MATLAB
Published by tiborauer almost 10 years ago

automaticanalysis -

- MATLAB
Published by tiborauer about 10 years ago

automaticanalysis - 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.

- MATLAB
Published by rhodricusack about 11 years ago

automaticanalysis - Release 4.21

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

- MATLAB
Published by rhodricusack about 11 years ago