Usage: 3dDespike [options] dataset Removes ‘spikes’ from the 3D+time input dataset and writes a new dataset with the spike values replaced by something more pleasing to the eye.
[see -corder option for description of the curve]
[see -NEW option for a different & faster fitting method]
- Compute the MAD of the difference between the curve and
the data time series (the residuals).
- Estimate the standard deviation ‘sigma’ of the residuals
as sqrt(PI/2)*MAD.
For each voxel value, define s = (value-curve)/sigma.
- Values with s > c1 are replaced with a value that yields
a modified s’ = c1+(c2-c1)*tanh((s-c1)/(c2-c1)).
c1 is the threshold value of s for a ‘spike’ [default c1=2.5].
- c2 is the upper range of the allowed deviation from the curve:
s=[c1..infinity) is mapped to s’=[c1..c2) [default c2=4].
Options:
- -ignore I = Ignore the first I points in the time series:
- these values will just be copied to the output dataset [default I=0].
- -corder L = Set the curve fit order to L:
the curve that is fit to voxel data v(t) is
k=L [ (2*PI*k*t) (2*PI*k*t) ]- f(t) = a+b*t+c*t*t + SUM [ d * sin(——–) + e * cos(——–) ]
k=1 [ k ( T ) k ( T ) ]where T = duration of time series; the a,b,c,d,e parameters are chosen to minimize the sum over t of |v(t)-f(t)| (L1 regression); this type of fitting is is insensitive to large spikes in the data. The default value of L is NT/30, where NT = number of time points.
- -cut c1 c2 = Alter default values for the spike cut values
- [default c1=2.5, c2=4.0].
- -prefix pp = Save de-spiked dataset with prefix ‘pp’
- [default pp=’despike’]
- -ssave ttt = Save ‘spikiness’ measure s for each voxel into a
- 3D+time dataset with prefix ‘ttt’ [default=no save]
- -nomask = Process all voxels
- [default=use a mask of high-intensity voxels, ]
[as created via ‘3dAutomask -dilate 4 dataset’].
- -dilate nd = Dilate ‘nd’ times (as in 3dAutomask). The default
- value of ‘nd’ is 4.
-q[uiet] = Don’t print ‘++’ informational messages.
- -localedit = Change the editing process to the following:
- If a voxel |s| value is >= c2, then replace the voxel value with the average of the two nearest non-spike (|s| < c2) values; the first one previous and the first one after. Note that the c1 cut value is not used here.
-NEW
- = Use the ‘new’ method for computing the fit, which
should be faster than the L1 method for long time series (200+ time points); however, the results are similar but NOT identical. [29 Nov 2013] * You can also make the program use the ‘new’
- method by setting the environment variable
- AFNI_3dDespike_NEW
- to the value YES; as in
- setenv AFNI_3dDespike_NEW YES (csh) export AFNI_3dDespike_NEW=YES (bash)
- If this variable is set to YES, you can turn off the ‘-NEW’ processing by using the ‘-OLD’ option.
- –>>* For time series more than 500 points long, the
‘-OLD’ algorithm is tremendously slow. You should use the ‘-NEW’ algorith in such cases.
- ** At some indeterminate point in the future, the ‘-NEW’
- method will become the default!
Caveats: * Despiking may interfere with image registration, since head
movement may produce ‘spikes’ at the edge of the brain, and this information would be used in the registration process. This possibility has not been explored or calibrated.
does NOT happen, and in fact, despiking seems to help!
registration! [Hint: open 2 AFNI controllers, and turn Time Lock on.]
automatic parallelizer software toolkit, which splits the work across multiple CPUs/cores on the same shared memory computer.
by a network (e.g., OpenMP doesn’t work with ‘cluster’ setups).
your system. You can control this value by setting environment variable OMP_NUM_THREADS to some smaller value (including 1).
using all CPUs available. ++ However, on some systems (such as the NIH Biowulf), it seems to be
necessary to set OMP_NUM_THREADS explicitly, or you only get one CPU.
count, since using more than (say) 16 threads is probably useless.
since OpenMP queries this variable BEFORE the program actually starts. ++ You can’t usefully set this variable in your ~/.afnirc file or on the
command line with the ‘-D’ option.
it was coded. You’ll have to experiment on your own systems!
The number of CPUs on this particular computer system is ...... 16.
The maximum number of CPUs that will be used is now set to .... 7.
++ Compile date = Dec 16 2015