Usage:
------
ExamineXmat is a program for examining the design matrix
generated by 3dDeconvolve.
The examination can be done interactively, by entering your
selections in a GUI (-interactive). Alternately, you can send the output to
an image file (-prefix). The title of the plot in the image contains the
filename and the number of regressors shown/total number.
The subtitle contains the various condition numbers of interest:
Rall for the entire matrix
Rall-motion for the matrix without motion parameters
Rall-roni for the matrix without any regressors of no interest
Rviewed for the part of the matrix displayed in the graph
More help is available in interactive usage mode.
Examples --- :
--------------
#Get some sample data
curl -o demo.X.xmat.1D \
afni.nimh.nih.gov/pub/dist/edu/data/samples/X.xmat.1D
#PDF output may not work on some machines
ExamineXmat -prefix t1.pdf -input demo.X.xmat.1D
ExamineXmat -prefix t2.jpg -input demo.X.xmat.1D -select ALL_TASKS
ExamineXmat -prefix t3.png -input demo.X.xmat.1D -select tneg tpos
ExamineXmat -prefix t4.jpg -input demo.X.xmat.1D -select MOTION tneg
ExamineXmat -prefix t5.jpg -input demo.X.xmat.1D -select tneg 3 35:38
#interactive mode
ExamineXmat
ExamineXmat -input demo.X.xmat.1D
ExamineXmat -input demo.X.xmat.1D -select tneg
#To save the last image you see interactively
ExamineXmat -input demo.X.xmat.1D -interactive \
-prefix t6.jpg -select tneg tpos
Options in alphabetical order:
------------------------------
-cprefix CPREFIX: Prefix of cor image only
-h: this help message
-help: this help message
-input 1Dfile: xmat file to plot
-interactive: Run examine Xmat in interactive mode
This is the default if -prefix is not given.
If -interactive is used with -prefix, the last
plot you see is the plot saved to file.
-msg.trace: Output trace information along with errors and notices
-pprefix PPREFIX: Prefix of plot image only
-prefix PREFIX: Prefix of plot image and cor image
-select SELECTION_STRING: What to plot.
Selection Strings:
To select regressors, you can use regressor indices or regressor
labels. For example, say your tasks (and therefore regressors)
are labeled "house", "face", "random"
Then to view house and face regressors only, select:
"house, face" or "house face" or "h fa" etc.
You can also use regressor indices (start at 0)
So you can select "0, 5, 10:12" for regressors 0, 5, 10, 11, and 12
You can also combine strings and integers in the same selection.
Commas, semicolons, and quotes are ignored.
Alternately you can specify special strings:
'ALL': The entire matrix
'ALL_TASKS': All task regressors
'RONI': All regressors of no interest (baseline+motion)
'BASE': All baseline regressors
'MOT': All motion regressors
-show_allowed_options: list of allowed options
-verb VERB: VERB is an integer specifying verbosity level.
0 for quiet (Default). 1 or more: talkative.
