General

Run on app on Linux, Mac and Windows. (Windows requirement could be fulfilled by Slicer Qdec module).

done

GUI-less module to support usage with XNAT (dan marcus, tim olsen) and usage with Slicer3 (steve pieper and ron kikinis)

done

XNAT: support for local XNAT and client-server XNAT

Input

done

selection of SUBJECTS_DIR (default taken from enviro on startup)

done

selection of an average subject (default is fsaverage)

done

parse an input file of stats engine input parameters

Stats Engine

done

output files tarballable and able to load (saving all parameters used to create output)

support for writing out the fsgd and contrasts without forcing an analysis

must work with more than two levels in a discrete factor (up to 11, which is the current default max)

allow saving the design covariance matrix

Display

support for correcting for multiple comparisions:

done

-- incorporate False Discovery Rate (FDR)

-- clustering/GRF: at least generate a script which can be run

show residual FWHM

done

hide green-cross hairs (so that it is not visible when a snapshot is taken)

lock rotation to x,y,z axes (so that spinning the brain is easier)

done

make sure Ctrl-left click always selects a point on the surface (as OpenGL point selector has no concept of our brain surface, and can pick outside points)

vertex data scatter plot:

-- allow saving the plot display and data

-- save plot in .eps format

-- keep plots a constant width, so snapshots are consistent (that is, don't change size from point to point to make room for varying label name widths)

-- allow setting min and max axis values

done

ROI selection (see Jenni's use case, #7)

mouse selection keys should match those in tksurfer (brucef)

optionally display Christophe annotations