v0.0.8 (July 10, 2015)

Model workflow

• Upgraded the model workflow to be compatible with FSL 5.0.7 and
  later. If you upgrade lyman, you will have to upgrade your FSL
  installation (i.e. it does not maintain backwards compatibility with
  older FSL). You should also upgrade to nipype 0.10. The main
  advantage of upgrading should be increased memory performance in the
  model estimation.

Registration workflow

• Added the ability to do cross-experiment registration, e.g. in the
  case where you have a functional localizer. This is accomplished
  through the -regexp flag in run_fmri.py. For example, the
  cmdline run_fmri.py -exp A -regexp B -regspace epi -timeseries
  will combine the func-to-anat matrices from experiment A and the
  anat-to-func matrix from the first run of experiment B, placing the
  experiment A files in a common space with experiment B files.

Fixed-effects workflow

• The fixed effects analysis no longer crashes when a subject did not
  have any observations for an event.

Mixed-effects workflow

• The mixed effects workflow now excludes empty images, allowing you
  to run it on a group where some subjects did not have any
  observations for a specific event/contrast.
• Updated the mixed effects boxplot code for compatibility with
  seaborn 0.6.

Anatomy snapshots script

• Added plots of the native white and pial surfaces
• Surface plots are now saved in one image file with all views, and
  the subplot size is automatically inferred to maximize the usage of
  space
• Added ventral views to the surface images
• Changed how the surface normalization is summarized. The new
  visualization highlights vertices where the binarized curvature
  value is different between the normalized subject and template
• Remove the "-noclose" option, as better ways to avoid the problem
  that motivated it have been identified.

Note that there are corresponding changes in ziegler that are needed to
properly view the new images, and there isn't backwards compatibility
with the old outputs. This script can be rerun on older lyman analyses
without affecting any results.

Surface snapshots script

• Changed how the individual frames of the surface snapshots are
  stitched together to maximize the use of space. This (and the
  changes in the anatomy snapshots script) rely on some new functions
  in lyman.tools.plotting that may be generally useful.
• Remove the "-keep-open" option, as better ways to avoid the problem
  that motivated it have been identified, and removed the "-no-window"
  option, as it is not clear whether this ever worked.