lyman: 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.