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5.3.0

New general features

  • aas_processBIDS generates subject names without "subj-"
  • aas_processBIDS and aa_export_toBIDS supports T2-weighted and diffusion data
  • aaq_qsub and aaq_matlab_pct are based on the same setting aap.directory_conventions.poolprofile which refers to a more standard profile rather than to a custom function
  • module domain and modality is changed dynamically according to the input
  • processing ASL data
  • ignoreseries is implemented
  • improved compatibility with MATLAB R2015a
  • improved compatibility with SPM8
  • stand-alone:
    • pragmas added to support building stand-alone version
    • aa_build_standalone to generate new functions with actualised pragmas
  • aamod_math supports
    • series of operations
    • arithmetic operations (+,-,*,/)

New features for structural

New features for Diffusion

New features for fMRI

Bugfixes

  • aaq_matlab_pct can launch arbitrary number of workers
  • handling multiple structurals (e.g. ME-FLASH)
  • aamod_epifromnifti handles
    • 3D NIfTI source
    • path relative to rawdatadir
    • manual header
  • aamod_secondlevel_threshold:
    • default threshold is set to p = 0.05 FWE-corrected
    • output for each first-level contrasts
  • aa_export_toBIDS handles
    • Diffusion data without DICOM header
    • fMRI data without events

5.2.0

New general features

  • MTI and sepcial_sessions) has benn moved to session domain and thus can be missing
  • aamod_get_dicom_* modules can now also edit DICOM fields
  • bounding box can be specified for aamod_norm_write* modules
  • aamod_norm_write* modules can process deformations
  • aamod_roi_extract* has option to use either the space of the data or the ROI
  • subjects with different sessions can be analysed
    • aamod_firstlevel_contrasts can automatically assign contrasts, unless uniquebysession is used. ⚠️ Contrast names must be unique both within- and across-sessions!
  • aamod_coreg_general is prepared for session domain and 4D NIfTI
  • killed and finished jobs will not be deleted
  • queue viewer is optional
  • aaparallel parameters has been added
  • aaq_matlab_pct has been tested on MATLAB 2015a
  • aaq_matlab_pct accepts
    • aaparallel parameters
    • external poolprofile function specified in aap.directory_conventions.poolprofile
    • pass aaworker
  • TFCE (external) has been updated

New features for fMRI

New features for MEG

Bugfixes

5.1.0

New general features

  • aa_export_toBIDS export raw data from aa pipeline in BIDS format (limited functionality)

New features for structural

  • automatic inputstream detection (and renaming) for aamod_roi_valid_structural

New features for fMRI

New features for MEG

Bugfixes

5.0.0 (branch v5 initial)

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>] (e.g. '+1xTASK|-1xREST' or '+1xTASKp1|-1xRESTm1'). N.B.: It requires regressor names with UPPERCASE letters only!

Bugfixes

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

4.3.1

Bugfix

4.3.0 (branch devel-share)

Copyrights

  • Sorting external/extrafunctions
  • Acknowledging externals in README.json

New general features

  • Dynamic modification of streams (aas_renamestream)

  • Selected_sessions now works also for branching

  • From NIfTI

    • 3D NIfTI inputs are fully supported
    • NIfTI fieldmaps are supported (aamod_fieldmapfromnifti)
    • BIDS datasets are supported (partial)
    • aamod_fsl_reorienttoMNI

New features for fMRI

  • New fMRI example to demonstrate some (new) features: (aa_user_fmri_advanced)

    • Specifying structural series
    • Explaining Motion FingerPrint instead of simple mocoparameters in design
    • Automatic slicetiming with exact timing from DICOM header (autodetectSO)
    • DARTEL normalisation
    • Activation maps projected to surface using FreeSurfer (aamod_firstlevel_threshold_register2FS)
    • Second-level GIFT (aamod_secondlevel_GIFT)
  • automatic temporal modulation

  • aamod_firstlevel_model: option to save residual

  • Despiking with BrainWavelet (aamod_waveletdespike)

  • aamod_maths

  • aamod_temporalfilter

New features for MEG

  • Diagnostics (courtesy to Rik Henson)
  • Update examples: aa_user_meg.m, aa_user_meg_connect
  • Maxfilter (aamod_meg_maxfilt) allows getting HPI from a session
  • Maxfilter (aamod_meg_maxfilt) accepts custom calibration files
  • Better delegeation of denoising tasks:
    • aamod_meg_denoise_ICA_1: runs ICA
    • aamod_meg_denoise_ICA_1: thresholds and removes
  • Epoching: aas_add_meg_event and aamod_meg_epochs
  • Averaging: aamod_meg_average

Improving robustness

  • Code development

    • Simplifying code
      • Setting modality --> aas_getfile_bystream automatically detects sessions based on modality
      • Avoid eval
      • Avoid spm_jobman
    • Removing 'orphan' functions
    • Update: spm_mods based on SPM12 r6470
  • Running

    • Compatibility with MATLAB pre-r2012b (local execution only)
    • qsub cleans jobs from previous execution
    • Iterative file retrieval (aap.options.maximumretry)
    • Specifying streams as diagnostic (aas_garbagecollection will not touch them)
    • aaworker
      • More efficient folder handling:
        • aaworker folders are created in ~/.aa (hidden) folder and
        • aaworker folders are cleaned up regularly after specified time (aap.options.aaworkercleanup)
      • aaworker structure is passed during qsub
  • Summaries

    • Add default message for "Motion correction summary"
    • Rename "First level contrasts" to "First level thresholded maps"

Convenience/Ease of access

  • Code development

  • Setting up

    • aaClass provides links to "the aa manuscript", to "the aa website" and to examples
    • Allow specification of subject in the whole UMS in the same way: aas_addcontrast, aas_addcovariate, aas_addevent, aamod_dartel_createtemplate
    • aap.options.checktasksettingconsistency: Check whether settings have changed since the last execution and re-run the task accordingly regardless of the doneflag (experimental!)
    • and are saved in the aap_parameters.mat file as fields aap.internal.aapversion and aap.internal.aappath
  • Running

    • qsub error provides links to code
    • GUI for qsub
    • aap.options.verbosity:
      0 - Does not show any message (still crashes in case of error)
      1 - Shows errors only
      2 - Shows every message (default)
  • Results

    • Vertical workflow chart
    • More consistent (and nicer ) graph of contrasts
    • aamod_firstlevel_threshold creates overlays along all three axes

4.2 (branch devel-share initial)

Described in "the aa manuscript"

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