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

volumetric analysis

be able to save analyzed data to a different directory, and load in analyzed data from a directory

get rid of the Subjects and Design panels. Instead, use a Wizard interface to load a table, check subjects, set the average subject name, choose measures, and specify other options. This will allow more room for GUI elements, as well as potentially have some context-sensitive help by dividing the steps into their own pages and having a "Help" button for each page.

add menu item to download XNAT result directly from website

Input / Subjects tab:

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

put labels on the 'continuous factors' graph

allow the graph contents to be saved to a TIFF

allow the user to zoom in on the graph contents

connect 'exclude subject' option (right-click) to something that actually excludes the subject

error checking: after a table is loaded, check that the expected number of levels for a factor was found, also check that there are no one-level discrete factors

Stats Engine / Design tab:

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

put mri_glmfit shell output in the view frame

have a live search text field to find measures

have explicit "None" option

have a way to display the contrast matrix

have a method to categorize measurement names. This could be done by using a naming scheme where categories are divided by a string token, e.g. Category|Name. The user would be able to hide or show all measures in a category in order to simplify the measurement lists.

allow the user to mark a measurement as a nuisance variable in the Design panel. In the Display panel, this would prevent any contrast question containing the text of that variable from showing up in the list

GUI for defining the contrast matrix

Question generator

Display tab:

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)

done

optionally display alternative annotations

display raw average thickness data, via 'mri_concat --i y.mgh --mean --o y-mean.mgh'

load and display gamma.mgh. Add a control to "View signfigance of gamma" for a contrast, and mask the gamma to the contraste values over the current threshold

option to take a screen shot with the color bar

change the Display pane viewing area into a split pane. Move the plotting window into the bottom frame, so you can see it at the same time as the surface

enter number of degrees of rotation (default 90deg)

in fsgd plot, display R-value slope

print fsgd plot as tiff or eps

dump vertex data for a fsgd plot