v1.0.3 Core working pipelines

Changes in this release

• Add support for subject-level parameters. This is mostly for experimental purposes.
• Use the more robust subject id instead of subject label to query XNAT for BIDS.
• correct bug for situation where only one matrix defined in collate group pipeline.
• Add ability to use external scripts outside of python ecosystem. A matlab example is provided.

v1.0.2 Core working pipelines

Changes in this release

• Add capability to run adhoc reports based on python or bash scripts
• Provide functionality for adding prefixes to group table headers

v1.0.1 Core working pipelines

Changes in this release

• Add capability to use an existing created fieldmap in basil pipeline
• Provide capability to extract measures from json, csv and txt files
• Add ability to use custom prefixes based on creating pipeline when collating csv files across a subject
• Capability to collate and merge two tables across all subjects
• Provide ability to use subject specific basil params - mostly for debugging purposes
• Add eddy params file based on cuda workflow for qsiprep pipeline
• Add the 10-node arterial atlas to available atlases
• Include mriqc pipeline to PANpipelines

v1.0.0 Core working pipelines

Changes in this release

• Add support to specify unique EDDY params for a subject
• Provide support for approach based on FSL's fsl_prepare_fieldmap to calculate fieldmap from 2 mag + 2 phase acquisitions from ME GRE to be used in BASIL pipeline
• Provide support for the incorporation of additional masks when calculating atlas measures. This allows multiple masks to be used at once e.g. the chemical shift segmentation and a grey matter mask.
• Provide support for use of FSL instead of ANTS to perform transformation. In certain cases in with multiple non-linear warp fields there was loss of accuracy when the non-linear transforms were converted to ANTS and utilized.

v0.9.9 Core working pipelines

Changes in this release

• Provide option to perform shift in T1 space while calculating segmentation for chemical shift artefact
• Include pepolar fieldmap support in Basil pipeline for possible situations where MEGRE is missing but DWI-RPE exists.

v0.9.8 Core working pipelines

Changes in this release

• Added support for slice to volume motion correction in eddy params
• Added support for chemical shift identification method that uses scalp surface.
• Increased granularity of echo-spacing definition to shared project level and provide option for retrieving echo-spacing from bids metadata
• Added shared project info to processing to relate subjects to original PAN projects

v0.9.7 Core working pipelines

Changes in this release

• Add support for segmenting asl artefact (chemical shift) and excluding the artefact region from average ASL

v0.9.6 Core working pipelines

Changes in this release

• Use bids filter to specify session and fieldmaps for fmriprep processing
• Add functionality to force bids download even if subject files exist on HPC. This will be necessary for processing fmriprep using dwei generated fieldmaps that will be generated on the XNAT

v0.9.5 Core working pipelines

Changes in this release

• Specify session for asl processing and attempt to terminate processing if fieldmap not found
• Use bids filter to specify session for dwi processing
• Add support for subject exclusions. Prevent pipeline dependencies from affecting deployment if parent pipeline already run

v0.9.4 Core working pipelines

Changes in this release

• This is a minor release. Just added logic to download TemplateFlow templates at the beginning of the pipeline run.