internal-tools update

Bump internal-tools version from 1.0.10 -> 1.0.12, addressing two issues:

• Missing outlier .mat files in DCANBOLDProcessing
• Docker build failure due to broken NeuroDocker ANTs link

Pin bids-validator version

This release is a quick fix to pin the version of bids-validator to 1.14.0, as current versions are incompatible with the Python 3.6 in the pipeline (see related issue: DCAN-Labs/abcd-hcp-pipeline#117 ). For future releases, we plan to use Pipfiles to avoid similar issues with Python dependencies.

Hotfix for Matlab MCR path error in v0.2.9

FIX: Matlab path error in DCANBOLDProcessing in v0.2.9 due to MCR path not matching the changed MCR version in external-tools (R2017a -> R2016b).

Add compiled Matlab code for dcan_bold_processing zero-padding hotfix

Adds updated dcan_bold_processing binaries with the zero-padding fix, which were omitted from v0.2.8.

v0.2.8: dcan_bold_processing update (add zero-padding to BOLD bandpass filter)

Changes from v0.2.7:

• ENH: Update dcan_bold_processing to v4.0.11 -- adds zero-padding to BOLD bandpass filtering step

This version contains updated time-series after re-applying the bandpass filter to the BOLD data. The new implementation includes zero padding to the BOLD data to minimize distortions in the edges of the time series. It’s important to note that this is not a bug, but rather an improvement. This release does not invalidate previous results, it reduces variance towards the beginning and end of the time-series data. In the previous release, those frames are discharged since are labeled as "outliers" in the provided mask. Using these updated data those frames at the end will not be discharged if the increased variance was related to the "edge effect", so users should be able to include more data in their analyses now.

v0.2.7

Changes from v0.2.6:

ENH: Update to internal-tools v1.0.8 / dcan_bold_processing v4.0.10
FIX: bandstop filter now works when filter range exceeds Nyquist frequency
ENH/FIX: report correct pipeline version with --version; report pipeline version to stdout at beginning of each stage

v0.2.6

• --multi-template-dir now defaults to using the included JointLabelCouncil templates
• Zenodo integration fix; current and future releases should be now archived correctly at https://zenodo.org/record/5484201

v0.2.5: Hotfix for syntax error in FreeSurfer

Updates dcan-macaque-pipeline to v0.1.1; fixes syntax error in FreeSurfer that occurred for certain combinations of --make-white-from-norm-t1 and --hyper-normalization-method. Error was observed in nhp-abcd-bids-pipeline v0.2.2, but likely affects versions from v0.2.0 through v0.2.4.

Dockerfile update

Change to build (Dockerfile) only. No change to function.

Documentation update (again)

• update README.md references to old Docker Hub repo (dcanlabs) to new repo (dcanumn)
• link pipeline stage summary doc from within README.md