CBU AA 5.4.0, August 2020

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

The major change in this release is to implement a toolbox functionality for supporting libraries like EEGLab and SPM. The long-term vision here is to only have libraries that a particular module needs on the path at any time, rather than requiring the kitchen sink on the path throughout. This change will break your defaults file, since some paths have moved from <aap><directory_conventions<spmdir>, <eeglabdir>, and <fieldtripdir> to <toolbox>. The solution if you're using the new user-specific defaults approach is to remove this file (by default something like mv ~/.aa/aap_parameters_user.xml ~/.aa/aap_parameters_user.xml.bak should work), and re-run to seed a new defaults file from the updated CBSU defaults. If you have a project-specific defaults file this will need updating manually.

CBU users can find this release under /imaging/local/software/AA/release-5.4.0_202008

CBU AA 5.4.0, October 2019

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

The major advance in this version is to fully support our new CENTOS7 cluster with the SLURM scheduler. Beyond this we made a few changes to accommodate the CamCAN pipelines, to hopefully remove the need for an independent CamCAN AA version. There are also various bug fixes, as listed below.

CBU users can find this release under /imaging/local/software/AA/release-5.4.0_201910

• Ensure that AA runs without SPM on the path, and that the AA-specified SPM version is respected. There was a bug where various SPM functions were called before SPM was added to the path by AA, which caused crashes if the user didn't have SPM on the path, and incorrect behaviour if the user had a different SPM version on their path than what they had specified in AA with the spmdir option. It was basically possible for the same user script to end up using different SPM versions in localsingle and qsub.
• Stop crashes when new ifconfig version is encountered in e.g. aas_writedoneflag (this caused crashed on new Centos7 cluster).
• Add the 'isrenameable' flag to many ROI processing modules (necessary for CamCAN pipeline)
• Update CBU defaults to run on new Centos7 cluster
• Bump SPM version to latest release (r7487)
• Add support MEG pipelines with maxfilter on new SLURM scheduler
• handle absent meminfo shell function (e.g. on CSH-derived shells) more gracefully
• Various minor adjustments to accommodate AA functionality at other sites (Surrey, RHUL) - we won't cover these in detail here since they don't affect CBU.

CBU AA 5.4.0, March 2019

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

This version is largely a bug fix release, which addresses issues with the previous version that was deployed at CBU (commit cc2e390, stored under /imaging/local/software/AA/release-5.4.0_201809 on the CBU imaging system):

• Fix bugs with CSH-based shells.

• Changed stream naming in DKI / DTI modules for consistency - the old 'normalised_grey' and 'native_grey' streams are now just one 'grey' stream. This makes AA more composable - you can work in native or MNI template space as you wish by renaming this stream appropriately.

• aas_export_toBIDS is now much more flexible with e.g. first-level model export

• aamod_firstlevel_threshold and aamod_secondlevel_threshold now support flexible overlays and templates

CBU AA 5.4.0, September 2018

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).

CBU AA 5.4.0, July 2018

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 2ed6c78, stored under /imaging/local/software/AA/release-5.4.0_201806 on the CBU imaging system):

• Bug fix - roi_extract modules (e.g., diffusion, MTR pipelines). If you have been using AA to do ROI analysis you may want to consider re-running.

• New functionality - basic RSA in the CosmoMVPA toolbox. If you are interested in doing MVPA with AA you may also want to look at this repo.

• Under the hood improvements to qsub, stand-alone AA

CBU AA 5.4.0, June 2018

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 2704399, stored under /imaging/local/software/AA/release-5.4.0_201804 on the CBU imaging system):

• Minor bug fix in DKI toolbox, used by diffusion pipeline.

• Bug fixes to 4D conversion. We now preserve nifti header information more accurately, which should help prevent crashes in the diffusion pipelines and missing header information in exported BIDS data (really a bug fix in SPM's 3D >> 4D converter spm_file_merge, which we include here)

• Lots of under-the-hood improvements to qsub. Running jobs on the cluster should hopefully be faster and more robust now.

• Now compatible with Matlab R2017a (we are waiting for Mathworks bug fixes to 2018a before moving to that)

• Now defaults to the latest version of SPM12 and the EEGLAB toolbox.

• The following old modules have been removed. Do let us know if you were actually using one of these:

D       aa_modules/aamod_firstlevel_model_nodicom.xml
D       aa_modules/aamod_firstlevel_model_nodicom_MVPaa.xml
D       aa_modules/aamod_firstlevel_modelestimate.xml
D       aa_modules/aamod_firstlevel_modelestimate_saveresids.xml
D       aa_modules/aamod_firstlevel_modelspecify.m
D       aa_modules/aamod_firstlevel_modelspecify.xml
D       aa_modules/aamod_firstlevel_modelspecify_explicitmask.xml
D       aa_modules/aamod_imcalc.m
D       aa_modules/aamod_mirrorandsubtract.m
D       aa_modules/aamod_ppi_model.m

CBU AA 5.4.0, April 2018

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 d607c46, stored under /imaging/local/software/AA/release-5.4.0_201802 on the CBU imaging system):

• Improvements to diffusion pipelines - should overcome bugs some users have been experiencing

• Various improvements for handling non-CBU, non-Siemens data.

• Fix various crash bugs caused by changes to built-ins in recent Matlab versions.

• The following new modules (have a look if the names sound intriguing):

A       aa_modules/aamod_LI.m
A       aa_modules/aamod_applyVDM.m
A       aa_modules/aamod_autoidentifyseries_philips.xml
A       aa_modules/aamod_diffusion_applyVDM.xml
A       aa_modules/aamod_diffusion_convert_fieldmaps.xml
A       aa_modules/aamod_diffusion_fieldmap2VDM.xml
A       aa_modules/aamod_diffusion_get_dicom_fieldmap.xml
A       aa_modules/aamod_firstlevel_LI.xml
A       aa_modules/aamod_secondlevel_LI.xml

CBU AA 5.4.0, February 2018

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 334d46a, stored under /imaging/local/software/AA/release-5.4.0 on the CBU imaging system):

• qsub is now faster, more responsive, and easier to debug (thanks Darren)

• BIDS import is a lot more feature complete (thanks Tibor and me). If you plan to share data it can actually be a good idea to -start- your analysis by exporting the raw data to BIDS using cbu2bids, and then import the BIDS-format data to AA for processing. This way your AA script can be shared along with your BIDS data and everything will just work. In my experience this also helps get your AA pipeline running sooner, because when your code starts with importing BIDS you circumvent some of AA's less robust modules (dicom parsing and conversion).

• The following new modules (have a look if the names sound intriguing):

git diff --name-status 334d46adddc80347f4dfe580ca22de8ef8cbe3fd | grep ^A | grep aa_modules/
A aa_modules/aamod_diffusion_applytopup.m
A aa_modules/aamod_diffusion_applytopup.xml
A aa_modules/aamod_firstlevel_model_collapsepredictors.m
A aa_modules/aamod_firstlevel_model_collapsepredictors.xml
A aa_modules/aamod_structural_smoothsegment.xml