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: #117 ). For future releases, we plan to use Pipfiles to avoid similar issues with Python dependencies.

v0.1.4

Resolves a couple outstanding issues, plus some repo maintenance. No changes to image processing from the previous release.

Changelist:
DOC: Update and migrate documentation to ReadTheDocs (#93, #103)
ENH: Updated CustomClean ABCD template included, for use with v0.1.x of this pipeline (DCAN-Labs/CustomClean#8)
FIX: In CustomClean JSON templates, wildcards in relative filepaths are now recognized as intended (DCAN-Labs/CustomClean#8)
FIX: Study template arguments now passed to PostFreeSurfer correctly (#97)
MISC: New issue reporting template (#93)

Version bumps:
DCAN-HCP 2.0.0 -> 2.0.1
internal-tools 1.0.10 -> 1.0.11
CustomClean 0.0.0 -> 2.0.3

Recompile Matlab code from v0.1.2

The zero-padding hotfix from v0.1.2 has been re-compiled with Matlab 2016b

Update to internal tools with DBP v.4.0.11

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.

Update internal tools and external software

Update Matlab version and make bug fix in filtered movement regressors code of DBP to enable processing of data with high TR.

Update dcan_bold_processing, ExecutiveSummary; add --session-id option, more

NOTE: Dockerhub release of this and future abcd-hcp-pipeline versions are at the new University of Minnesota DCAN repo: https://hub.docker.com/repository/docker/dcanlabs/abcd-hcp-pipeline Prior releases will continue to be available at https://hub.docker.com/repository/docker/dcanlabs/abcd-hcp-pipeline.

NOTE 2: Though image processing until the DCANBOLDProcessing state is unaltered from previous versions (v0.0.0 through v0.0.4), intermediate and output filenames from the FMRIVolume stage onward have changed. Due to this, if reprocessing data previously processed on an older pipeline version, we recommend first backing up or removing the old output, then running the pipeline from the beginning. It is also possible to rerun previously processed data starting at FMRIVolume by deleting all directories in <sub>/<ses>/files except T1w, T2w (if applicable), and MNINonLinear (with the exception of MNINonLinear/Results, which should be deleted).

Changes from v0.0.4:

• regular expressions for extracting BIDS fields from filenames revised for consistency with dcan_bold_processing, this fixes several issues with BIDS task and run naming in v0.0.4 and prior.

• new option --session-id to filter BIDS input to a specific session or list of sessions

• timeseries output from FMRIVolume stage and onward now include "ses-" label

• dcan_bold_processing updated from hotfix/issue27 branch to stable release v4.0.8; see changelist here: https://github.com/DCAN-Labs/dcan_bold_processing/releases

• ExecutiveSummary updated from v0.0.1 to v2.2.10; see changelist here: https://github.com/DCAN-Labs/ExecutiveSummary/releases

Minor update to DCAN BOLD Processing and MRE version

DCAN BOLD Processing has been updated to expand the range of task names that can be run. Previous versions have issues if a "-" is included in the task name or if the task name is too long.

The Matlab Runtime Environment version has also been updated from v91 to v92

Bugfix to v0.0.2

The Dockerfile contained a no longer used path for Connectome Workbench and refused to build. This bugfix version 0.0.3 fixes that. Now the Docker image is built again at:

https://hub.docker.com/r/dcanlabs/abcd-hcp-pipeline

Minor fixes and cleanup

Users discovered some broken pieces which were fixed. See pull request commit for full details.

v0.0.1: Singularity hotfix

this allows use of singularity containers, with appropriate new steps in the documentation
tested against the latest version of Singularity, v3.1.0