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CBU AA 5.4.0, September 2018
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@jooh jooh released this 20 Sep 12:42
· 289 commits to master since this release
v5.4.0_201809
cc2e390

Informal CBU release - to ease reproducibility and data sharing, we make releases whenever the deployed version on the CBU imaging system changes.

This version includes the following improvements, relative to the previous version that was deployed at CBU (commit 76cfca4, stored under /imaging/local/software/AA/release-5.4.0_201807 on the CBU imaging system):

This is a big update! We try to achieve two major objectives, which I will cover first. Then I'll mention a few minor changes that have also crept into this update.

Major changes

  1. Easier to get started with aa - the examples are shorter, have documentation, and should just run (famous last words) on a new machine, thanks to many under the hood changes to how AA defines file paths, and even downloads open datasets as needed.

  2. Rudimentary automated testing that runs through the examples above (see aatest.m).

To achieve this we have added many under-the-hood features:

  • shell expansion in aarecipe - you can reference any shell $variable or $(expression) in any XML field, and the result will be evaluated at run-time.

  • aarecipe looks for ~/.aa/aap_parameters_user.xml if no defaults.xml file is specified in the user script. If this file does not exist, aarecipe can generate it by asking the user to select one of the existing defaults as the parent. This should make it easier to maintain a custom AA setup across different user scripts.

  • default aap.acq_details.root - use the above functionality to place data in sensible default locations ($HOME/aa in defaults.xml, /imaging/$USER/aa in defaults_CBSU.xml).

  • We now setenv an SPMDIR shell variable to make it easy to reference SPM-relative paths in defaults and tasklists, using the above expansion functionality.

  • BIDS import improvements: select custom events.tsv column for first-level model regressor definition, select sub-set of subjects.

  • handy functions for automatically downloading the aa demo and BIDS 114 datasets from OSF, if needed.

Minor changes

  • all roi_extract modules now expect input from the rois stream instead of the ROIFile option. This makes AA more modular and flexible. You will need to modify user scripts by adding aas_addinitialstream.

  • quieter, less repetitive logging, especially when using aas_shell

  • new modules to reorient nifti header dimensions to the format expected by fslview and similarly stupid viewers.

  • Update CBSU default with new version of various toolboxes. Lock versions to specific versions rather than referencing 'latest' for greater reproducibility. Set more sensible defaults (e.g., numdummies should arguably default to 0).

  • removed old code: aa_config, aas_configforSPM12, many old examples.

  • tidy-up - change all file endings and line breaks to unix.

  • tidy-up - co-locate example user scripts and tasklists in the example folder. I think this makes more sense since these files are used together only.

  • update readme to be somewhat more current.

  • examples updated to use the currently recommend fMRI preprocessing pipeline (segment8 normalisation rather than norm_noss, coreg_extended rather than standard coreg).

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