Deletions are marked like this. | Additions are marked like this. |
Line 15: | Line 15: |
|| || update wiki page documentation, and create an 'advanced QDEC' page listing all the extras || | || || update wiki page documentation, and create an 'advanced QDEC' page listing all the features not described in main tutorial || |
[wiki:QdecProject top]
Feature List
priority |
General: |
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 |
done |
be able to save analyzed data to a different directory, and load in analyzed data from a directory |
volumetric analysis |
|
|
build on Linux, Mac and Windows independent of freesurfer. (Windows requirement could be fulfilled by Slicer Qdec module). |
|
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 |
|
update wiki page documentation, and create an 'advanced QDEC' page listing all the features not described in main tutorial |
|
|
|
|
|
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 (qdec_glmfit) |
done |
put labels on the 'continuous factors' graph |
done |
allow the factor plot to be saved to postscript |
done |
connect 'exclude subject' option (right-click) to something that actually excludes the subject |
done |
allow the user to exclude subjects based on continuous factor range and discrete factor class |
wizard to import aseg and aparc data from subjects stats files and merge into qdec.table.dat |
|
|
allow the user to zoom in on the graph contents |
|
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) |
done |
fixup question generation to include ', accounting for <factor>' |
done |
display Degrees Of Freedom in the current design |
done |
allow selection of either DODS or DOSS in overall design |
|
allow selection of either DODS or DOSS per factor (requires mri_glmfit change) |
|
support for writing out the fsgd and contrasts without forcing an analysis |
|
must work with more than two levels in a discrete factor, at least three |
|
allow saving the design covariance matrix |
|
put mri_glmfit shell output in the view frame |
|
have a live search text field to find measures |
|
display the design matrix in grid-block form |
|
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 |
|
|
|
|
|
|
|
Contrast tab: |
create a Contrast tab to break-apart Design matrix phase from Contrast matrix phase, allowing selection of particular contrast matrices (main effects, interactions, etc.) |
|
|
display a list of selectable nuisance factors (the list of prior-selected discrete and continuous factors) |
|
display the contrast and design matrices in grid-block form |
|
GUI for defining the contrast matrix, raw entry with text showing regressors, use the form used in SPSS |
|
Question generator - fill-in-the-blank |
|
make mri_glmfit run in a separate thread |
|
|
|
|
|
|
|
Display tab: |
done |
ROI selection (see Jenni's use case, #7) |
done |
optionally display alternative annotations |
done |
hide green-cross hairs (so that it is not visible when a snapshot is taken) |
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) |
done |
print fsgd plot as postscript |
done |
correcting for multiple comparisions: False Discovery Rate (FDR) |
done |
save vertex plot in postscript format |
|
correcting for multiple comparisions: clustering/GRF- at least generate a script which can be run |
|
show residual FWHM |
|
lock rotation to x,y,z axes (so that spinning the brain is easier) |
|
allow saving the vertex plot data |
|
keep vertex 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) |
|
in vertex plot, allow setting min and max axis values |
|
in vertex plot, display R-value slope |
|
mouse selection keys should match those in tksurfer (brucef) |
|
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 signficance of gamma" for a contrast, and mask the gamma to the contrast 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, or, alternatively, have two notebook tabs: surface and plot |
|
enter number of degrees of rotation (default 90deg) |
|
functionality to answer these questions: |
|
-- is a particular parcellation significant compared to the rest of the brain? |
|
-- where is the slope of a selected vertex significantly greater than other areas of the brain? |
|
|
|
|
|
|
|
|