Deletions are marked like this. | Additions are marked like this. |
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|| '''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'''|| 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 || |
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|| '''done''' || be able to save analyzed data to a different directory, and load in analyzed data from a directory || | ||'''done'''|| be able to save analyzed data to a different directory, and load in analyzed data from a directory || |
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|| '''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 || || '''done''' || put labels on the 'continuous factors' graph || || '''done''' || allow the factor plot to be saved to postscript || |
||'''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 || ||'''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 || || || allow the user to exclude subjects based on continuous factor range and discrete factor class || |
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|| || connect 'exclude subject' option (right-click) to something that actually excludes the subject || | |
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|| '''done''' || output files tarballable and able to load (saving all parameters used to create output) || |
||'''done'''|| output files tarballable and able to load (saving all parameters used to create output) || ||'''done'''|| fixup question generation to include ', accounting for <factor>'|| |
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|| || have a way to display the contrast matrix || | || || display the design matrix in grid-block form || |
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|| || || || || || || || || || || '''''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 the contrast and design matrices in grid-block form || |
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||<rowbgcolor='#FF8080'> || fixup question generation to include ', regardless of <factor>'|| | |
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|| || || | |
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||'''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 || |
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|| '''done''' || -- incorporate False Discovery Rate (FDR) || | ||'''done'''|| -- incorporate False Discovery Rate (FDR) || |
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|| '''done''' || hide green-cross hairs (so that it is not visible when a snapshot is taken) || | |
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|| '''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) || | |
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|| '''done''' || ROI selection (see Jenni's use case, #7) || | |
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|| '''done''' || optionally display alternative annotations || | |
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|| '''done''' || print fsgd plot as postscript || | |
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[wiki:QdecProject top]
Feature List
priority |
General: |
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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 |
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done |
be able to save analyzed data to a different directory, and load in analyzed data from a directory |
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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. |
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add menu item to download XNAT result directly from website |
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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 |
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 |
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allow the user to exclude subjects based on continuous factor range and discrete factor class |
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allow the user to zoom in on the graph contents |
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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 |
wizard to import aseg and aparc data from subjects stats files and merge into qdec.table.dat |
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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>' |
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support for writing out the fsgd and contrasts without forcing an analysis |
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must work with more than two levels in a discrete factor, at least three |
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allow saving the design covariance matrix |
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put mri_glmfit shell output in the view frame |
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have a live search text field to find measures |
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display the design matrix in grid-block form |
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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. |
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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 |
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Contrast tab: |
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create a Contrast tab to break-apart Design matrix phase from Contrast matrix phase, allowing selection of particular contrast matrices (main effects, interactions, etc.) |
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display the contrast and design matrices in grid-block form |
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GUI for defining the contrast matrix, raw entry with text showing regressors |
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Question generator - fill-in-the-blank |
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make mri_glmfit run in a separate thread |
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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 |
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support for correcting for multiple comparisions: |
done |
-- incorporate False Discovery Rate (FDR) |
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-- clustering/GRF: at least generate a script which can be run |
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show residual FWHM |
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lock rotation to x,y,z axes (so that spinning the brain is easier) |
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vertex data scatter plot: |
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-- allow saving the plot display and data |
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-- save plot in .eps format |
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-- 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) |
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-- allow setting min and max axis values |
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mouse selection keys should match those in tksurfer (brucef) |
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display raw average thickness data, via 'mri_concat --i y.mgh --mean --o y-mean.mgh' |
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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 |
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option to take a screen shot with the color bar |
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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 |
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enter number of degrees of rotation (default 90deg) |
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in fsgd plot, display R-value slope |
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dump vertex data for a fsgd plot |
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functionality to answer these questions: |
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-- is a particular parcellation significant compared to the rest of the brain? |
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-- where is the slope of a selected vertex significantly greater than other areas of the brain? |
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