Version 1.8.1 Beta (Sep 17, 2021)¶
New Features & Pipeline Harmonization
ABCD-BIDS Pipeline Harmonization.
The ABCD-BIDS pipeline of the ABCD study can now be reproduced by running the ABCD preconfig in C-PAC.
CCS Pipeline Harmonization.
A new BOLD masking option,
CCS_Anatomical_Refined
, has been added. This has been adapted from the BOLD mask method from the CCS pipeline.New T1 masking options using Freesurfer have been added to facilitate the harmonization with the CCS pipeline.
A preconfigured pipeline that reproduces the CCS pipeline is now available.
fmriprep Pipeline Harmonization Updated.
The fmriprep-options preconfigured pipeline, which reproduces the fmriprep pipeline, has been updated to reflect recent changes.
Improvements
Further improvements to memory management for less frequent hanging have been integrated, in an ongoing process.
Freesurfer’s Recon-All functionality in C-PAC has been opened to further configurability.
More options for selecting a reference for slice-timing correction have been added.
Description and other meta-data fields have been added to some output JSON sidecar files in an ongoing process to make output data descriptors clearer.
DVARS calculation is now performed using AFNI 3dTto1d, increasing computation speed.
Manually inserting input data to a C-PAC output directory for ingress is now easier. A sidecar JSON containing meta-data will be produced for the data automatically if one is not provided.
For developers: improvements to the codebase have streamlined the process of adding new output data types to C-PAC through a central table, in line with recent v1.8 changes and the move to BIDS-Derivatives compliance.
Bug Fixes
Choosing On/Off for nuisance regression once again correctly produces the non-cleaned BOLD outputs in addition to any nuisance regression strategies.
Forking T1 and EPI based registration while simultaneously forking ANTs and FSL registration options no longer crashes the pipeline.
An error where the DVARS calculation step would cause the pipeline to hang has been resolved.
All nuisance regression choices are now available for EPI-registration based pipelines.
The
mem_gb
input parameter for memory allocation no longer overrides other memory selections, when left unspecified.The
selected_volume
option for motion correction reference is now working again.