v2.0.0

Lyman version 2 comprises a set major change to the library (and an essentially complete rewrite of the codebase). Major aspects of the changes are summarized here; more details are available throughout the collection of related pull requests.

• The preprocessing workflow now transforms all images into a cross-experiment functional template space that is defined in register with the Freesurfer anatomy. All spatial operations (motion-correction, unwarping, and transformation into template space) are applied in one step to minimize interpolation error.

• Preprocessing has been streamlined to involve mainly spatial transformations of the images, The various signal-processing operations (smoothing, temporal filtering, artifact detection) are now considered part of the modeling workflow, meaning that parameters that control these operations are model-specific. There are no longer separate "smoothed" and "unsmoothed" paths through the workflows.

• Model-fitting and contrast estimation are now implemented in Python, instead of FSL binaries (although univariate model fitting still uses the FILM GLS prewhitening algorithm).

• An experiment-independent template workflow has been added, and the reg and ffx workflows have been removed.

• There is no longer the concept of an "altmodel"; instead, different models are a first-class level of the lyman organization hierarchy.

• Lyman currently supports only HCP-style datasets that include a single pair of spin-echo EPI images with opposite phase encoding directions, which are used for unwarping susceptibility-induced distortions and registration to the anatomy.

• There is currently no support for anatomical normalization or group analyses.

• There is better support for experiments where subjects are scanned in multiple sessions.

• The contrast estimation code now properly handles contrasts between parameter estimates where one of the parameters is undefined in some runs.

• Spatial smoothing is performed using a novel algorithm that smooths in volume space using Gaussian weights determined by distance on the surface manifold.

• A number of static images that were generated for quality control have been removed, and others have been added.

• The command-line interface has changed so that all interaction happens through a single lyman command line script that has sub-modes corresponding to different workflows (and, in the future, other functionality such as results visualization).

• Automated test coverage of the codebase has been dramatically improved.

• Various aspects of the supporting library code has been moved from moss into lyman itself, and moss is no longer a dependency of lyman.