CPAC Version 1.0.0 Beta

Dear Colleagues,

We are happy to inform you that we recently released CPAC Version 1.0.0 Beta. You can update your existing installations of CPAC using instructions here and instructions for a fresh install of CPAC are here. Please let us know if you have any questions or feedback by posting to the forum.

The updates to CPAC in this new version include:

• CPAC now calculates network centrality derivatives using the new 3dDegreeCentrality, 3dEigenvectorCentrality, and 3dLFCD AFNI tools implemented by our developers. These implementations are optimized to minimize the memory requirements while speeding up computation time. If you have an already-existing installation of AFNI that does not have these newer tools, you can update your installation by running "@update.afni.binaries" from your AFNI installation directory.
• CPAC inputs can now be directly downloaded from and outputs can be directly uploaded to AWS S3 cloud storage.
• SLURM cluster resource scheduler compatibility added.
• We removed user specified segmentation thresholds from the segmentation workflow and instead rely on the default thresholds used by FSL's FAST tool. This removes the issue of choosing an appropriate threshold, which would previously result in no WM or CSF signals for nuisance correction.
• The GUI has been reorganized to simplify pipeline configuration, and specifically to improve handling of nuisance correction strategies and specifying ROIs for time series extraction and seed correlation analysis.
• Group-level analysis has been over-hauled to make it run more quickly, handle repeated measures, make entering contrasts more intuitive, and improve transparency in to the model generation process.
• Nipype and CPAC have been updated to use a resource aware scheduler that incorporates information about the amount of memory and cores currently available when choosing a pipeline step to run. This should maximize running different pipeline steps in parallel while reducing the occurrence of out-of-memory errors and system lock-ups.
• The output resolution in MNI space for statistical derivatives (e.g., ReHo, DC, etc) and 4D preprocessed functional data can be specified separately. The user can now also decide not to write the 4D preprocessed data into MNI space. Both of these steps can significantly reduce memory and disk space requirements.
• Improved logging.
• Column names of ROI time series files and file names for SCA outputs are now based on the unique identifier used for the ROI in the corresponding atlas, making it easier to relate the files back to the ROIs.
• For the subject list generated, we replaced the confusing "%s" identifiers in file path templates with {participant}, {site}, {session} to make generating these templates more user friendly.
• Added support for BIDS file structure.

Along with the updates to the code, we have made many much needed updates to the user documentation. We have also updated the cpac_resources.tar.gz file to include 4mm templates.

Updated user documentation for this release can be found here:
http://fcp-indi.github.io/docs/user/index.html

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

Regards,
The CPAC development team.

CPAC Version 0.3.9 Alpha

Please consult the User Guide for a full description of the new features and changes.

• 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.
  • The "mean of measure" regressor option can now be calculated using a specified mask, in addition to the option of using an automatically created mask for each individual.
  • 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. This will enable for example, including seperate regressors for white matter and CSF.
  • The statistical derivatives to be analyzed can now be specified for each group model, allowing the user more flexibility for using different group models (i.e. include different nuisance regressors) for different derivatives.
  • Better error checking and more informative error and warning messages have been added.

For a tutorial presentation on how to use CPAC's group-level analysis model builder, click here.

• New AWS functionality, which contain utilities for interacting with Amazon Web Services' S3 storage service, including upload, download, renaming 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. This will now result in a easy to understand error message.
• Fixed a bug where the cluster size for ReHo would not be properly saved in the pipeline configuration file.
• Updated the ANTS registration workflow to work with newer versions of ANTs and ITK.
• 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 and error messages for improper subject-list formatting and inputs.
• Introduced checks to determine whether the user has the 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 AFNI outputs would be written out in the wrong format resulting in a CPAC crash.

Along with the updates to the code, we have made many much needed updates to the user and developer documentation. We have also updated the cpac_resources.tar.gz file to include the missing templates for 1mm registration.

CPAC Version 0.3.8.1 Alpha

Release for archiving.

CPAC Version 0.3.8 Alpha

• Fixed a bug in which ANTS registration transforms were applied in the wrong order.
• "Treatment" coding has been enabled as an option in the Group Analysis Model Builder.
• Resolved several errors effecting warping Dual Regression outputs to standard space.
• SCA correlation maps now written out into 4D file instead of being stored into a 5D file (with the 4-dimension being a singleton).
• Fixed a bug in compCor nuisance regression in which WM and CSF time-series were not variance normalized, as implemented by the original paper.
• Updated the cpac_run.py script available in the scripts directory in order to reflect changes in how CPAC is run, update documentation, and enable users to invoke custom installs of Nipype and CPAC.
• Several GUI error fixes and improvements:
  • Introduced more descriptive error messages if the subject list is formatted or entered incorrectly.
  • Fixed an issue with input checking in the pipeline configuration editor.
  • Fixed an issue where saving an edited pipeline configuration file would require the user to re-load the file onto the pipeline list.
• Developer tools: Created a unit test created for the Network Centrality workflow.

CPAC Version 0.3.7 Alpha

• CPAC 0.3.7 has been migrated to a newer version of Nipype, version 0.10.0. The link is found below.
• ANTS anatomical registration now calculates and applies an additional transform which makes registration more robust to certain input images that may have had registration difficulties otherwise.
• Users can now set a custom number of cores to dedicate to anatomical registration when using ANTS, enabling faster registration speeds (just be careful not to assign more than you have!).
• Group analysis no longer requires symbolic links to be generated in order to run.
• Fixed the Network Centrality RAM shortage bug and improved stability of the Network Centrality code.
• Network Centrality now produces smoothed non-z-score-standardized outputs.
• Bug fixes concerning the GUI and pipeline configuration editor, including an issue where input file paths were checked in the pipeline configuration editor even when the associated workflows were turned off.

Nipype 0.10 is available here:
https://github.com/nipy/nipype/releases/tag/0.10.0

CPAC Version 0.3.6 Alpha

v0.3.6

Merge branch 'master' of https://github.com/FCP-INDI/C-PAC

CPAC Version 0.3.5 Alpha

Merge pull request #368 from FCP-INDI/0.3.5_development

0.3.5 development

version 0.3.2

Configurable PIpelines for the Analysis of Connectomes (CPAC). Version 0.3.2 Release.