C-PAC: CPAC Version 0.3.9 Alpha

• Major group analysis model builder upgrades:
  • f-tests are now fully integrated into the new model builder GUI.
  • Users can now provide their own custom, hand-coded contrasts matrix if they do not wish to use the model builder's contrast dialog box.
  • The mean of measure regressor option can now be calculated using a group-specific mask, in addition to the option to calculate it using the individual-specific mask.
  • A custom ROI mask file can now be provided with one or more ROIs - the mean of these ROIs will then be calculated and included as regressors in the model.
  • Derivatives to be run are now chosen for each group model, allowing the user to widely vary the type of analyses conducted within a single CPAC group analysis run.
  • Many new informative messages in the model builder GUI warning users of potential issues with the model being built before it lets group analysis run.

( Please consult the User Guide for a full description of the new model builder features and changes. )

• New AWS subpackage - subpackage containing utilities to interact with Amazon Web Services' S3 storage service. This subpackage provides for simple functions to assist in data upload, download, renaming of files. Additionally, it provides some tools for local file MD5 sums and AWS credentials fetching.
• Scrubbing now works properly.
• Pipeline speed-ups gained by ensuring ANTS-based symmetric anatomical registration only runs when necessary.
• Moved to Jenkinson's Mean Framewise Displacement (Mean FD) calculation for MeanFD-related measures.
• Made the output file structure for SCA outputs more clear.
• Changed the working directory structure for group analysis so that it is more clear.
• Fixed a bug where the skull-stripped brain was actually being used when the user selected to calculate the ANTS anatomical-to-template registration with the skull on.
• Fixed a bug in group analysis where not all of the selected derivatives would run in some cases.
• Fixed a bug where the pipeline would crash if the segmentation thresholds were set too high.
• Fixed a bug where the cluster size for ReHo would not be saved in the pipeline configuration file properly.
• Removed a parameter from the ANTS registration call that was no longer compatible with newer versions of the ITK framework.
• Fixed a bug where CPAC group-level analysis would not run on a single cluster node, even with "Run CPAC on a Cluster/Grid" turned off.
• Introduced more checks for improper subject-list formatting and inputs.
• Introduced checks which ensure the user has the main required software packages installed before starting a pipeline run.
• Fixed some bugs where users would run into obstacles when trying to run CPAC on certain installations.
• Fixed a bug where CPAC would sometimes crash during anatomical preprocessing when AFNI would write outputs in the wrong format.