Version 1.6.1 Beta (Feb 11, 2020)

NEW FEATURES

• Pre-configured Pipeline Library. C-PAC can now be easily run with a growing selection of pre-configured pipelines with the –preconfig flag. See the updated User Documentation for the pipelines available.

• Time Series De-spiking. C-PAC can now run AFNI 3dDespike at the beginning of functional preprocessing, if enabled. https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDespike.html

• Smooth to a Specific FWHM. C-PAC can now run AFNI BlurToFWHM as an option, alongside the original FSL-based smoothing option. https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBlurToFWHM.html

IMPROVEMENTS

• Temporal Filtering Configurability. The order in which temporal filtering is performed in the pipeline can now be toggled either before or after nuisance regression. If set to before, nuisance regressors are also filtered.

• tCompCor Configurability. Users can now choose polynomial regression of the time series, as well as configure the degree of brain mask erosion for tCompCor nuisance regression.

• BOLD Masking Configurability. The FSL-BET option for BOLD masking now has full access to configurable parameters.

• CSF Regressor Configurability. Ventricle mask refinement of CSF masks for CSF-based nuisance regression can now be toggled.

• More informative messages for when someone provides an incorrect AWS S3 link for input data.

FIXES

• Anatomical in template space QC images are now displayed properly in the QC Interface.

• The ‘scan’ and ‘selector’ buttons now work properly again in the QC Interface.

• Translation and rotation motion plots are now labeled correctly.

• A bug where the input data configuration would be formatted incorrectly when no BIDS directory JSON was present has been fixed.

• The “start_idx” pipeline field, which allows users to select the first time point in the time series, now works properly again.

• Fixed an error that would report a duplicate node name when running a FNIRT-based pipeline and ICA-AROMA at the same time.

In addition, the C-PAC Docker and Singularity images, as well as the AWS AMI, have all been updated. These provide a quick way to get started.

And as always, you can contact us here for user support and discussion: https://groups.google.com/forum/#!forum/cpax_forum