voxels in the functional brain image are followed through time.
Each voxel displays a pattern (of intensity variation) through time
that corresponds to the blood oxygen level in that particular location
at a particular time. These patterns can be compared to the predicted
hemodynamic response associated with a task. Afni 1-D files are
files that contain predicted hemodynamic responses to be correlated
to actual hemodynamic patterns displayed by our functional analyses.
Correlations between the predicted pattern and the pattern in each
voxel can then identify locations/voxels in the brain that appear
to be activated during the task.
is the program used to make these 1-D files. Ultimately, you want
waver to generate a file with a column of 80 numbers if you have
80 TRs (for example). Waver typically generates extra TRs at the
end of the output file that you don't need...so you'll need to examine
and edit the file in nedit (or another text editor) to make sure
that you have one value for each TR.
will provide information about how to use the program (see Appendix
99999 = missing values
is a sample command to create a base 1D file (the values you enter
here will be convolved with the ideal waveform):
-WAV -delaytime 0.0 -risetime 2.0 -dt 1.0 -inline 2@0 3@1 2@0 >
above line tells waver to create a text file with the following
tells waver to use the Cox special waveform as the hemodynamic default.
0.0 = Sets delay time, before the start of the hemodynamic (HD)
response, to 0 seconds.
-risetime 2.0 = Sets rise time (of the HD response) to 2
-dt 1.0 = Sets time step (TR) of output AND input to 1.0
-inline DATA = Read timeseries from command line DATA; convolve
with waveform to produce output DATA in the form of numbers and
count@value, as in "-inline 2@0 3@1 2@0" which
means a timeseries with 2 TRs at zero, then 3 TRs at one, then a
final 2 TRs at zero to be convolved with the HD waveform.
output of the waver command is normally sent to standard output
(it scrolls by you on the screen), but can be redirected with the
> to a file (in this case, fred.1D) that will be
created in the area you are currently working in.
is the file generated with the above command (the numbers represent
a standard hemodynamic response given the input parameters):
files will need to be edited, eg,
that in editing, you must keep track of the row number very accurately.
Many editors, including nedit, have an option to turn on a counter
to keep track of your row and column position
.turn it on:
Go to "preferences" in the nedit menu and select "statistics
line" or "show statistics". Cursor row and column
number will appear in the status line at the bottom of the nedit
our example, we requested 7 timepoints and waver generated 13. So
you will want to remove the last 6 values from the file:
may also involve dropping certain time periods from consideration
by inserting the number 99999 (make SURE you get all 5 9's in there)
in place of rows that will be dropped out. Usually you will 9999
out time blocks that encompass a particular stimulus. You can 99999
out rows after creating the file, or you can tell the waver command
to 99999 them out for you later. This is difficult to illustrate
with our hypothetical 7 second experiment, so lets image something
an experiment has 3 conditions: rest, control and hum. Imagine you
have 100 TRs: Each condition takes a certain number of TRs. Let's
say, for simplicity's sake, that TRs 1-10 occur during a rest, 11-20
occur during a control, 21-30 occur during hum and then the pattern
repeats twice more, followed by a final rest:
are, of course, not obligated by waver to make each condition last
for the same period of time (10 TRs in this example) or to put the
conditions into the same repetitive pattern, though you'll probably
choose a very regular pattern for the sake of good experimental
are some sample waver files for our imagined 100 TR experiment:
-WAV -delaytime 0.0 -risetime 2.0 -dt 1.0 -inline 10@0 10@1 10@1
10@0 10@1 10@1 10@0 10@1 10@1 10@0 > ContHum_Rest.1D
the above example, we are creating a file that compares rest (0)
to the active condition ('control' and 'hum' conditions are both
'active'). You'll need to remove extra TRs from the end.
we want to compare 'rest' to 'hum' and ignore the 'control' condition?
We could manually edit ContHum_Rest.1D so that control rows (11-20,
41-50, 71-80) were set to 99999 (and we might want to give the edited
version a new name). We could also use waver to create an alternative
file (and we'd need to remove extra TRs from the end):
-WAV -delaytime 0.0 -risetime 2.0 -dt 1.0 -inline 10@0 10@99999
10@1 10@0 10@99999 10@1 10@0 10@9999 10@1 10@0 > Hum_Rest.1D
this point, you should be able to figure out how to compare 'hum'
to 'control' (and ignore 'rest'); or, how to treat 'rest' and 'control'
as active conditions that you wish to compare to 'hum' as an inactive
condition, etc. Good luck.
waver [options] > output_filename
Creates an ideal waveform timeseries file. The output goes to stdout,
and normally would be redirected to a file.
(# refers to a number; [xx] is the default value)
-WAV = Sets waveform to Cox special [default] (cf. AFNI FAQ
list for formulas)
-GAM = Sets waveform to form t^b * exp(-t/c) (cf. Mark Cohen)
"expression" = Sets waveform to the expression given,
which should depend on the variable 't'.
e.g.: -EXPR "step(t-2)*step(12-t)*(t-2)*(12-t)"
N.B.: The peak value of the expression on the '-dt' grid will be
scaled to the value given by '-peak'; if this is not desired, set
'-peak 0', and the 'natural' peak value of the expression will be
options set parameters for the -WAV waveform.
-delaytime # = Sets delay time to # seconds 
-risetime # = Sets rise time to # seconds 
-falltime # = Sets fall time to # seconds 
-undershoot # = Sets undershoot to # times the peak [0.2]
(this should be a nonnegative factor)
-restoretime # = Sets time to restore from undershoot 
options set parameters for the -GAM waveform:
-gamb # = Sets the parameter 'b' to # [8.6]
-gamc # = Sets the parameter 'c' to # [0.547]
options apply to all waveform types:
-peak # = Sets peak value to # 
-dt # = Sets time step of output AND input [0.1]
default is just to output the waveform defined by the parameters
above. If an input file is specified by one of the options below,
then the time series defined by that file will be convolved with
the ideal waveform defined above -- that is, each nonzero point
in the input timeseries will generate a copy of the waveform starting
at that point in time, with the amplitude scaled by the input timeseries
= Outputs data in 2 columns, where the first column is time and
the second is the waveform. Without the -xyout option, waver produces
1 column, the waveform.
The two column option is useful for graphing.
infile = Read timeseries from *.1D formatted 'infile'; convolve
with waveform to produce output
N.B.: you can use a sub-vector selector to choose a particular column
of infile, as in
DATA = Read timeseries from command line DATA; convolve with waveform
to produce output DATA in the form of numbers and count@value, as
-inline email@example.com firstname.lastname@example.org email@example.com 1.0 firstname.lastname@example.org 2.0
which means a timeseries with 20 zeros, then 5 ones, then 30 zeros,
a single 1, 20 more zeros, and a final 2. [The '@' character may
actually be any of: '@', '*', 'x', 'X'. Note that * must be typed
as \* to prevent the shell from trying to interpret it as a filename
DATA = Read discrete stimulation times from the command line and
convolve the waveform with delta-functions at those times. In this
input format, the times do NOT have to be at intervals of '-dt'.
-dt 2.0 -tstim 5.6 9.3 13.7 16.4
specifies a TR of 2 s and stimuli at 4 times (5.6 s, etc.) that
do not correspond to integer multiples of TR. DATA values cannot
be negative. If the DATA is stored in a file, you can read it onto
the command line using something like
-tstim `cat filename`
where using the backward-single-quote operator of the usual
least one option is required, or the program will just print this
message to stdout. Only one of the 3 timeseries input options above
can be used.
you have the 'xmgr' graphing program, then a useful way to preview
the results of this program is through a command pipe like
>waver -dt 0.25 -xyout -inline 16@1 40@0 16@1 40@0 | xmgr
Using the cruder AFNI package program 1dplot, you can do something
>waver -GAM -tstim 0 7.7 | 1dplot -stdin
a square wave is desired, see the 'sqwave' program.