Version 2.0 Release

What's new?

• Introducing the Brain Imaging Data Structure (BIDS) to improve and standardize data organisation
• Improved batch processing, including independent T2 mapping
• Parallel computing for faster processing
• Cleaner processing output stream and verbose logging

Version 1.3.1 Release

• Fixed fMRI nibabel deprecation to allow fMRI processing
• Better adjecency matrix heatmap plotting

Version 1.3 Release

What's new?

• We fully switched to Docker containerization of the software
• Added slice-time correction
• Improved usage and manual

Version 1.2 Release

What's New?

Docker image

• Full release of our Docker image for easy cross-platform installation and usage of AIDAmri command line tools
• Updated manual

DTI processing

• Updated DTI codes to fit modern DSI-Studio releases
• Added legacy flags for batch processing and DTI connectivity to minimize conflict with deprecated naming and data type conventions (see help pages by running batchProg.py -h)

Version 1.1.2

What's New?

The following changes and improvements have been made:

Dockerfile beta is now available at the dockerdev branch. It is used to create an image to launch the pipeline without installing its dependencies on the host system manually. The following functions are accessible for now:

• Pipeline CLI client for command line usage of AIDAmri (the GUI is not supported for versions higher than v.1.1).
• Every registration, preprocessing and processing function for T2w, DTI and fMRI of the pipeline is supported.

To set-up and use the Dockerfile, please take a look at the Docker manual.

Version 1.1

What's New?

The following changes and improvements have been made:

1_PV2NIfTiConverter: pv_conv2Nifti.py

• Warnings corrected
• slice gap now included: the parameter VisuCoreSlicePacksSliceDist will be added to the slice (e.g. gap =0.1 mm and slice 0.5 mm will be added to a new slice with 0.6 mm)
• In addition: we have added an alternative and improved Bruker to Nifty converter (not fully integrated into AIDAmri yet).

2.1_T2PreProcessing: registration_T2.py

• Changed atlas allenBrain_annorsfMRI to split parental atlas annoVolume+2000_rsfMRI.nii.gz => also the T2w data is registered with the same atlas as fMRI and DTI data later on

Further Changes:

• Added a new batch_proc to automate the processing steps for the complete dataset
• Throughout the code minor issues were fixed (e.g. typos in the help functions)
• Added bin/3.2.1_DTIdata_extract
• Added bin/4.1_ROI_analysis

=> Details can be found in the updated manual

Credits

Alternative pv-reader and 4.1 ROI Analysis provided by courtesy of Michael Diedenhofen (Max Planck Institute for Metabolism Research, Cologne)

Version 1.0

Credits

4.1 ROI Analysis provided by courtesy of Michael Diedenhofen (Max Planck Institute for Metabolism Research, Cologne)